Compositions that specifically bind to colorectal cancer cells and methods of using the same

ABSTRACT

A unique transcription product, CRCA-1, and alternative translation products generated therefrom, are disclosed. The transcript and its translation products are markers for colorectal cells. Screening and diagnostic reagents, kits and methods for metastasized colorectal cancer are disclosed as are reagents, kits and methods for identifying adenocarcinomas as colorectal in origin. Compounds, compositions and methods of treating patients with metastasized colorectal cancer and for imaging metastasized colorectal tumors in vivo are disclosed. Compositions and methods for delivering active compounds such as gene therapeutics and antisense compounds to colorectal cells are disclosed. Vaccines compositions and methods of for treating and preventing metastasized colorectal cancer are disclosed.

This Application is a divisional of U.S. provisional application Ser.No. 08/908,643 filed Aug. 7, 1997 now U.S. Pat. No. 6,120,995, allowed.

FIELD OF THE INVENTION

The present invention relates to in vitro diagnostic methods fordetecting colorectal cancer cells, to kits and reagent for performingsuch methods. The present invention relates to compounds and methods forin vivo imaging and treatment of colorectal tumors. The presentinvention relates to methods and compositions for making and usingtargeted gene therapy, antisense and drug compositions. The presentinvention relates to prophylactic and therapeutic anti-colorectal cancervaccines and compositions and methods of making and using the same.

BACKGROUND OF THE INVENTION

Colorectal cancer is the third most common neoplasm worldwide. Themortality rate of newly diagnosed large bowel cancer approaches 50% andthere has been little improvement over the past 40 years. Most of thismortality reflects local, regional and distant metastases.

Surgery is the mainstay of treatment for colorectal cancer butrecurrence is frequent. Colorectal cancer has proven resistant tochemotherapy, although limited success has been achieved using acombination of 5-fluorouracil and levamisole. Surgery has had thelargest impact on survival and, in some patients with limited disease,achieves a cure. However, surgery removes bulk tumor, leaving behindmicroscopic residual disease which ultimately results in recrudescence.

Early detection of primary, metastatic, and recurrent disease cansignificantly impact the prognosis of individuals suffering fromcolorectal cancer. Large bowel cancer diagnosed at an early stage has asignificantly better outcome than that diagnosed at more advancedstages. Similarly, diagnosis of metastatic or recurrent disease earlierpotentially carries with it a better prognosis.

Although current radiotherapeutic agents, chemotherapeutic agents andbiological toxins are potent cytotoxins, they do not discriminatebetween normal and malignant cells, producing adverse effects anddose-limiting toxicities. Over the past decade, a novel approach hasbeen employed to more specifically target agents to tumor cells,involving the conjugation of an active agent to molecules which bindspreferentially to antigens that exist predominantly on tumor cells.These conjugates can be administered systemically and specifically bindto the targeted tumor cells. Theoretically, targeting permits uptake bycells of cytotoxic agents at concentrations which do not produce serioustoxicities in normal tissues. Also, selective binding to targeted tumorcells facilitates detection of occult tumor and is therefore useful indesigning imaging agents. Molecular targeting predominantly has employedmonoclonal antibodies generated to antigens selectively expressed ontumor cells.

Immunoscintigraphy using monoclonal antibodies directed attumor-specific markers has been employed to diagnose colorectal cancer.Monoclonal antibodies against carcinoembryonic antigen (CEA) labelledwith ⁹⁹Technetium identified 94% of patients with recurrent tumors.Similarly, ¹¹¹Indium-labelled anti-CEA monoclonal antibodiessuccessfully diagnosed 85% of patients with recurrent colorectalcarcinoma who were not diagnosed by conventional techniques.¹²⁵Iodine-labelled antibodies have been effective in localizing morethan 80% of the pathologically-confirmed recurrences by intraoperativegamma probe scanning.

Monoclonal antibodies have also been employed to target specifictherapeutic agents in colorectal cancer. Preclinical studiesdemonstrated that anti-CEA antibodies labelled with ⁹⁰Yttrium inhibitedhuman colon carcinoma xenografts in nude mice. Antibodies generated tocolorectal cancer cells and coupled to mitomycin C or neocarzinostatindemonstrated an anti-tumor effect on human colon cancer xenografts innude mice and 3 patients with colon cancer. Similar results in animalswere obtained with monoclonal antibodies conjugated to ricin toxin Achain.

Due to the sensitivity, specificity, and adverse-effect profile ofmonoclonal antibodies, the results obtained using monoclonalantibody-based therapeutics have shown them to be less than idealtargeting tools. Although monoclonal antibodies have been generated toantigens selectively expressed on tumors, no truly cancer-specificantibody has been identified. Most antigens expressed on neoplasticcells appear to be quantitatively increased in these compared to normalcells but the antigens are nonetheless often present in normal cells.Thus, antibodies to such determinants can react with non-neoplastictissues, resulting in significant toxicities. Also, antibodies arerelatively large molecules and consequently, often evoke an immuneresponse in patients. These immune responses can result in significanttoxicities in patients upon re-exposure to the targeting agents and canprevent targeting by the monoclonal due to immune complex formation withdegradation and excretion. Finally, binding of antibodies to tumor cellsmay be low and targeted agents may be delivered to cells in quantitiesinsufficient to achieve detection or cytotoxicity.

There remains a need for reagents, kits and methods for screening,diagnosing and monitoring individuals with colorectal cancer,particulalry metastasized colorectal cancer. There is a need forreagents, kits and methods for identifying and confirming that a cancerof unknown origin is colorectal cancer and for analyzing colon tissueand colorectal cancer samples to identify and confirm colorectal cancerand to determine the level of migration of such cancer cells. Thereremains a need for compositions which can specifically targetmetastasized colorectal cancer cells. There is a need for imaging agentswhich can specifically bind to metastasized colorectal cancer cells.There is a need for improved methods of imaging metastasized colorectalcancer cells. There is a need for therapeutic agents which canspecifically bind to metastasized colorectal cancer cells. There is aneed for improved methods of treating individuals who are suspected ofsuffering from colorectal cancer cells, especially individuals who aresuspected of suffering from metastasis of colorectal cancer cells. Thereis a need for vaccine composition to treat and prevent metastasizedcolorectal cancer. There is a need for therapeutic agents which canspecifically deliver gene therapeutics, antisense compounds and otherdrugs to colorectal cells.

SUMMARY OF THE INVENTION

The invention relates to isolated nucleic acid molecules that comprise aCRCA-1 transcript.

The invention relates to isolated nucleic acid molecules that comprisenucleic acid sequences that encode a substantially pure CRCA-1translation product or a functional fragment thereof. The inventionrelates to isolated nucleic acid molecules that comprise nucleic acidsequences that encode a substantially pure proteins that have amino acidsequences shown in SEQ ID NOs: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23,25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59,61, 63, 65, 67, 69, 71, 73, 75, 77, 79 and 81.

The invention relates to isolated nucleic acid molecules that comprisenucleic acid sequences shown in SEQ ID NO:1 or a functional fragmentthereof. More particularly, the invention relates to isolated nucleicacid molecules that consist of a functional fragment of SEQ ID NO:1comprising 12–150 nucleotides.

The invention relates to pharmaceutical compositions that comprisenucleic acid molecule that comprise a CRCA-1 transcript.

The invention relates to pharmaceutical compositions that comprisenucleic acid molecule that comprise nucleic acid sequence shown in SEQID NO:1 or a functional fragment thereof in combination with apharmaceutically acceptable carrier.

The invention relates to a recombinant expression vector comprising thenucleic acid molecule that has a nucleotide sequence that comprises SEQID NO:1 or a functional fragment thereof.

The invention relates to a host cell comprising a recombinant expressionvector comprising the nucleic acid molecule that has a nucleotidesequence that comprises SEQ ID NO:1 or a functional fragment thereof.

The invention relates to an oligonucleotide molecule comprising anucleotide sequence complimentary to a nucleotide sequence of SEQ IDNO:1 or a functional fragment thereof. More particularly, the inventionrelates to an oligonucleotide molecule comprising a nucleotide sequencecomplimentary to a functional fragment of SEQ ID NO:1 comprising 5–50nucleotides, 10–40 nucleotides, 15–25 nucleotides, 10–150 nucleotides,or 18–28 nucleotides.

The invention relates to isolated antibodies that bind to an epitope ona CRCA-1 translation product.

The invention relates to a substantially pure CRCA-1 translation productor a functional fragment thereof.

The invention relates to a substantially pure proteins that have aminoacid sequences shown in SEQ ID NO:2–81.

The invention relates to pharmaceutical compositions comprising asubstantially pure CRCA-1 translation product or a functional fragmentthereof.

The invention relates to pharmaceutical compositions comprising asubstantially pure protein having amino acid sequences shown in SEQ IDNOs: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37,39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73,75, 77, 79 and 81 in combination with a pharmaceutically acceptablecarrier.

The invention relates to isolated antibodies that bind to an epitope ona protein having the amino acid sequence of SEQ ID NOs: 3, 5, 7, 9, 11,13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47,49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79 and 81.

The present invention relates to in vitro methods of determining whetheror not an individual has metastasized colorectal cancer cells. Thepresent invention relates to in vitro methods of examining samples ofnon-colorectal tissue and body fluids from an individual to determinewhether or not a colorectal cancer specific transcript or a translationproduct thereof, CRCA-1, which is specific to colorectal cells includingcolorectal tumor cells, is being expressed by cells outside of thecolorectal tract. The presence of a CRCA-1 translation product or of theCRCA-1 transcript outside the intestinal tract is indicative ofexpression of CRCA-1 and is evidence that the individual is sufferingfrom metastasized colorectal cancer.

The present invention relates to in vitro methods of determining whetheror not tumor cells are colorectal in origin. The present inventionrelates to in vitro methods of diagnosing whether or not an individualsuffering from cancer is suffering from colorectal cancer. The presentinvention relates to in vitro methods of examining samples of tumorsfrom an individual to determine whether or not CRCA-1, which is specificto colorectal cells including colorectal tumor cells, is being expressedby the tumor cells. The presence of a CRCA-1 translation product or ofthe CRCA-1 transcript is indicative of expression of CRCA-1 is evidencethat the individual is suffering from colorectal cancer.

The present invention relates to in vitro kits for practicing themethods of the invention and to reagents and compositions useful ascomponents in such in vitro kits of the invention.

The present invention relates to conjugated compounds which comprises aCRCA-1 translation product binding moiety and a radiostable activemoiety.

The present invention relates to a pharmaceutical composition comprisinga pharmaceutically acceptable carrier or diluent, and a conjugatedcompound which comprises a CRCA-1 translation product binding moiety anda radiostable active moiety.

The present invention relates to a method of treating an individualsuspected of suffering from metastasized colorectal cancer comprisingthe steps of administering to said individual a pharmaceuticalcomposition comprising a pharmaceutically acceptable carrier or diluent,and a therapeutically effective amount of a conjugated compound whichcomprises a CRCA-1 translation product binding moiety and a radiostableactive moiety.

The present invention relates to a pharmaceutical composition comprisinga pharmaceutically acceptable carrier or diluent, and a conjugatedcompound which comprises a CRCA-1 translation product binding moiety anda radioactive active moiety.

The present invention relates to a pharmaceutical composition comprisinga pharmaceutically acceptable carrier or diluent, and conjugatedcompound that comprises a CRCA-1 translation product binding moiety anda radioactive active moiety wherein the conjugated compound is presentin an amount effective for therapeutic or diagnostic use in humanssuffering from colorectal cancer.

The present invention relates to a method of radioimaging metastasizedcolorectal cancer cells comprising the steps of first administering toan individual suspected of having metastasized colorectal cancer cells,a pharmaceutical composition that comprises a pharmaceuticallyacceptable carrier or diluent, and conjugated compound that comprises aCRCA-1 translation product binding moiety and a radioactive activemoiety wherein the conjugated compound is present in an amount effectivefor diagnostic use in humans suffering from colorectal cancer and thendetecting the localization and accumulation of radioactivity in theindividual's body.

The present invention relates to a method of treating an individualsuspected of suffering from metastasized colorectal cancer comprisingthe steps of administering to said individual a pharmaceuticalcomposition comprising a pharmaceutically acceptable carrier or diluent,and a therapeutically effective amount of a conjugated compound whichcomprises a CRCA-1 translation product binding moiety and a radioactiveactive moiety.

The present invention relates to conjugated compounds which comprises aCRCA-1 translation product binding moiety and a active moiety whichcomprises an antisense molecule.

The present invention relates to a pharmaceutical composition comprisinga pharmaceutically acceptable carrier or diluent, and a conjugatedcompound which comprises a CRCA-1 translation product binding moiety andan active moiety which comprises an antisense molecule.

The present invention relates to a method of treating an individualsuspected of suffering from colorectal cancer comprising the steps ofadministering to a such an individual, a pharmaceutical compositioncomprising a pharmaceutically acceptable carrier or diluent and atherapeutically effective amount of a conjugated compound whichcomprises a CRCA-1 translation product binding moiety and an activemoiety which comprises an antisense molecule.

The present invention relates to a method of preventing colorectalcancer in an individual comprising the steps of administering to saidindividual a pharmaceutical composition comprising a pharmaceuticallyacceptable carrier or diluent and a prophylactically effective amount ofa conjugated compound which comprises a CRCA-1 translation productbinding moiety and an active moiety which comprises an antisensemolecule.

The present invention relates to unconjugated compositions comprises aliposome that includes CRCA-1 translation product ligands on its surfaceand an active component encapsualted therein.

The present invention relates to a pharmaceutical composition comprisinga pharmaceutically acceptable carrier or diluent, and an unconjugatedcompositions comprises a liposome that includes CRCA-1 translationproduct ligands on its surface and an active component encapsualtedtherein.

The present invention relates to a method of treating an individualsuspected of suffering from a disease, condition or disorder of thecolon or of prevcenting such a disease, disorder or condition in anindiidual who is at risk of developing the same, comprising the steps ofadministering to the colon a such an individual, a pharmaceuticalcomposition comprising a pharmaceutically acceptable carrier or diluent,and an unconjugated compositions that comprises a liposome that includesCRCA-1 translation product ligands on its surface and an activecomponent encapsualted therein.

The present invention relates to a method of delivering an active agentto colon cells of an individual, including metastasized colorectalcancer cells comprising the steps of administering to such anindividual, a pharmaceutical composition comprising a pharmaceuticallyacceptable carrier or diluent, and an unconjugated compositions thatcomprises a liposome that includes CRCA-1 translation product ligands onits surface and an active component encapsualted therein.

The present invention relates to compositions that comprise CRCA-1translation product ligands in combination with an active component.

The present invention relates to a pharmaceutical composition comprisinga pharmaceutically acceptable carrier or diluent and a composition thatcomprise CRCA-1 translation product ligands in combination with anactive component.

The present invention relates to a method of treating an individualsuspected of suffering from a disease, condition or disorder of thecolon or of prevcenting such a disease, disorder or condition in anindividual who is at risk of developing the same, comprising the stepsof administering to the colon a such an individual, a pharmaceuticallyacceptable carrier or diluent and a composition that comprise CRCA-1translation product ligands in combination with an active component.

The present invention relates to a method of delivering an active agentto colon cells of an individual, including metastasized colorectalcancer cells comprising the steps of administering to such anindividual, a pharmaceutical composition comprising a pharmaceuticallyacceptable carrier or diluent and a composition that comprise CRCA-1translation product ligands in combination with an active component.

The present invention relates to an isolated protein comprising at leastone epitope of a CRCA-1 translation product. In some embodiments, theisolated protein comprises a CRCA-1 translation product. In someembodiments, the isolated protein consists of a CRCA-1 translationproduct.

The present invention relates to vaccines which comprise such proteinsand a pharmaceutically acceptable carrier or diluent.

The present invention relates to a haptenized protein comprising atleast one epitope of a CRCA-1 translation product. In some embodiments,the haptenized protein comprises a CRCA-1 translation product. In someembodiments, the haptenized protein consists of a CRCA-1 translationproduct.

The present invention relates to vaccines which comprise such haptenizedproteins and a pharmaceutically acceptable carrier or diluent.

The present invention relates to nucleic acid molecules that encode aprotein comprising at least one epitope of a CRCA-1 translation product.In some embodiments, the nucleic acid molecule encodes a protein thatprotein comprises a CRCA-1 translation product. In some embodiments, thenucleic acid molecule encodes a protein that consists of a CRCA-1translation product. In some embodiments, the nucleic acid moleculeencodes the CRCA-1 transcript. In some embodiments, the nucleic acidmolecule is a plasmid.

The present invention relates to vaccines which comprise such nucleicacid molecules and a pharmaceutically acceptable carrier or diluent.

The present invention relates to vectors that comprise nucleic acidmolecules that encode a protein comprising at least one epitope of aCRCA-1 translation product. In some embodiments, the vector comprises anucleic acid molecule that encodes a protein that protein comprises aCRCA-1 translation product. In some embodiments, the vector comprises anucleic acid molecule that encodes a protein that consists of a CRCA-1translation product. In some embodiments, the vector comprises a nucleicacid molecule that is the CRCA-1 transcript. In some embodiments, thevector is a virus or a bacterial cell. In some embodiments, the vectoris a recombinant vaccinia virus.

The present invention relates to vaccines which comprise such vectorsand a pharmaceutically acceptable carrier or diluent.

The present invention relates to killed or inactivated cells orparticles that comprise a protein comprising at least one epitope of aCRCA-1 translation product. In some embodiments, the killed orinactivated cells or particles vector comprise the transmembrane domainof the human ST receptor protein. In some embodiments, the killed orinactivated cells or particles comprise a CRCA-1 translation product. Insome embodiments, the killed or inactivated cells or particles consistof a CRCA-1 translation product. In some embodiments, the killed orinactivated cells or particles vector is a killed or inactivatedcolorectal tumor cells.

The present invention relates to vaccines which comprise such killed orinactivated cells or particles and a pharmaceutically acceptable carrieror diluent.

The present invention relates to haptenized killed or inactivated cellsor particles that comprise a protein comprising at least one epitope ofa CRCA-1 translation product. In some embodiments, the haptenized killedor inactivated cells or particles comprise a CRCA-1 translation product.In some embodiments, the haptenized killed or inactivated cells orparticles consist of a CRCA-1 translation product. In some embodiments,the haptenized killed or inactivated cells or particles vector is akilled or inactivated colorectal tumor cells.

The present invention relates to vaccines which comprise such haptenizedkilled or inactivated cells or particles and a pharmaceuticallyacceptable carrier or diluent.

The present invention relates to methods of treating individualssuffering from metastasized colorectal cancer. The method of the presentinvention provides administering to such an individual a therapeuticallyeffective amount of a vaccine of the invention. The invention relates tothe use of such vaccines as immunotherapeutics.

The present invention relates to methods of treating individualssusceptible metastasized colorectal cancer. The method of the presentinvention provides administering to such an individual an amount of avaccine of the invention effective to prevent or combat metastasizedcolorectal cancer. The present invention relates to the use of thevaccines of the invention prophylactically.

BRIEF DESCRIPTION OF THE FIGURE

FIG. 1 (SEQ ID NO:83) shows the nucleotide sequence of the human STreceptor mRNA, GenBank™ Accession #S57551. The gray shaded area is thesequence deleted in CRCA-1 transcript including one of the two boxed“GG” sequences or one G from each box. The start codon, ATG which isnucleotides 118–119–120 of the sequence is the initiation codon for STreceptor protein expression. The CRCA-1 transcript is missing a 142nucleotide sequence spanning nucleotides 192–333, 193, 334 or 194–335.Thus unique sequences of the CRCA-1 transcript not in found ST receptormRNA include nucleotides 191–192–193–336, 191–192–335–336 or191–334–335–336 as set forth in the sequence listing. These 4 nucleotidesequences are all identical, A-G-G-C, and correspond to nucleotides110–111–112–113 of SEQ ID NO:1.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

As used herein, the terms “ST” and “native ST” are used interchangeablyand are meant to refer to heat-stable toxin (ST) which is a peptideproduced by E. coli, as well as other organisms. STs are naturallyoccurring peptides which 1) are naturally produced by organisms, 2) bindto the ST receptor and 3) activate the signal cascade that mediatesST-induced diarrhea.

As used herein, the terms “ST receptor”, “guanylyl cyclase C receptor”and “GCC receptor” are meant to refer to the receptors found oncolorectal cells, including local and metastasized colorectal cancercells, which bind to ST. In normal individuals, ST receptors are foundexclusively in cells of intestine, in particular in cells in theduodenum, small intestine (jejunum and ileum), the large intestine,colon (cecum, ascending colon, transverse colon, descending colon andsigmoid colon) and rectum.

As used herein, the terms “colorectal cancer-associated transcript” and“CRCA-1 transcript” are meant to refer to an alternative form of themRNA for the ST receptor produced by transcription of the human STreceptor gene. The CRCA-1 transcript possesses an alternative sequencefrom that of the ST receptor encoding-mRNA. CRCA-1 transcript preferablyhas a nucleotide sequence set forth in SEQ ID NO:1. CRCA-1 transcript isfound in colorectal cells, including local and metastasized colorectalcancer cells. In normal individuals, CRCA-1 transcript have been foundexclusively in cells of intestine, in particular in cells in theduodenum, small intestine (jejunum and ileum), the large intestine,colon (cecum, ascending colon, transverse colon, descending colon andsigmoid colon) and rectum.

As used herein, the term “functional fragment” as used in term“functional fragment of a CRCA-1 transcript product” is meant tofragments of CRCA-1 transcript which are functional with respect tonucleic acid molecules with full length sequences. For example, afunctional fragment may be useful as an oligonucleotide or nucleic acidprobe, a primer, an antisense oligonucleotide or nucleic acid moleculeor a coding sequence. Functional fragments of the CRCA-1 transcript areunique compared to other known nucleic acid molecules, in particularfunctional fragments of the CRCA-1 transcript are unique compared tonucleic acid sequence of the ST receptor mRNA. The nucleotide sequenceencoding human ST receptor protein is disclosed in FIG. 1 (SEQ IDNO:82), SEQ ID NO:84, and F. J. Sauvage et al. 1991 J. Biol. Chem.266:17912–17918 which are incorporated herein by reference. The deletedsequence which results in the generation for the CRCA-1 transcript isdisclosed in FIG. 1 (SEQ ID NO:83) and SEQ ID NO:85. Thus, thefunctional fragments of the CRCA-1 include specific sequences not foundon the ST receptor mRNA. Such unique sequences include the sequences oneither side of the deletion thus forming a unique sequence relative tothe ST receptor mRNA sequence. Accordingly, a functional fragment willinclude nucleotides 110–113 of SEQ ID NO: 1. It is preferred that theunique sequence additionally include 5–10 or more sequences 5′ tonucleotide 110 and 5–10 or more sequences 3′ to nucleotide 113.Oligonucleotides and other fragments of the CRCA-1 transcript which havesequences of function fragments include nucleotides 110–113 of SEQ IDNO: 1 and may additionally include sequences 5′ and 3′ to the uniquefour nucleotide sequences formed by the deletion. For example, a PCRprimer having 8–28 nucleotides including a unique sequence for CRCA-1,i.e. a functional fragment having 8 nucleotides may include nucleotidesequence 106–113 or 110–117 or an 8 nucleotide sequence generated fromthe intermediate sequences, i.e. 107–114, 108–115 or 109–116, or afunctional fragment having 28 nucleotides may include nucleotidesequence 86–113 or 110–137 or a 28 nucleotide sequence generated fromthe intermediate sequences. Similarly, other functional fragments ofCRCA-1 transcript would include 110–113 of SEQ ID NO: 1 as part of afragment of SEQ ID NO: 1. With respect to CRCA-1 specific primers, setsof such primers may include one unique fragment of CRCA-1 transcript andone primer which is not specific for a unique CRCA-1 sequence providedthat such a pair of primers can be used to amplify a CRCA-1 specificsequence.

As used herein, the terms “colorectal cancer-associated translationproducts” and “CRCA-1 translation products” are meant to refer totranslation products set forth in SEQ ID NOs:2–81. CRCA-1 translationproducts are found in colorectal cells, including local and metastasizedcolorectal cancer cells. In normal individuals, CRCA-1 translationproducts have been found exclusively in cells of intestine, inparticular in cells in the duodenum, small intestine (jejunum andileum), the large intestine, colon (cecum, ascending colon, transversecolon, descending colon and sigmoid colon) and rectum.

As used herein, the term “functional fragment” as used in the term“functional fragment of a CRCA-1 translation product” is meant tofragments of CRCA-1 translation products which function in the samemanner as proteinaceous compounds with full length sequences. Forexample, an immunogenically functional fragment of a CRCA-1 comprises anepitope recognized by an anti-CRCA-1 translation product antibody. Aligand-binding functional fragment of a CRCA-1 comprises a sequencewhich forms a structure that can bind to a ligand which recognizes andbinds to a CRCA-1 translation product.

As used herein, the term “epitope recognized by an anti-CRCA-1translation product antibody” refers those epitopes recognized by ananti-CRCA-1 translation product antibody which does not recognizeepitopes of non-CRCA-1 translation products, i.e. does not cross reactwith non-CRCA-1 proteins.

As used herein, the term “antibody” is meant to refer to complete,intact antibodies, and Fab fragments and F(ab)₂ fragments thereof.Complete, intact antibodies include monoclonal antibodies such as murinemonoclonal antibodies, chimeric antibodies and humanized antibodies.

As used herein, the term “CRCA-1 translation product ligand” is meant torefer to compounds which specifically bind to a CRCA-1 translationproduct. Antibodies that bind to a CRCA-1 translation product are CRCA-1translation product ligands. An CRCA-1 translation product ligand may bea protein, peptide or a non-peptide.

As used herein, the term “active agent” is meant to refer to compoundsthat are therapeutic agents or imaging agents.

As used herein, the term “radiostable” is meant to refer to compoundswhich do not undergo radioactive decay; i.e. compounds which are notradioactive.

As used herein, the term “therapeutic agent” is meant to refer tochemotherapeutics, toxins, radiotherapeutics, targeting agents orradiosensitizing agents.

As used herein, the term “chemotherapeutic” is meant to refer tocompounds that, when contacted with and/or incorporated into a cell,produce an effect on the cell including causing the death of the cell,inhibiting cell division or inducing differentiation.

As used herein, the term “toxin” is meant to refer to compounds that,when contacted with and/or incorporated into a cell, produce the deathof the cell.

As used herein, the term “radiotherapeutic” is meant to refer toradionuclides which when contacted with and/or incorporated into a cell,produce the death of the cell.

As used herein, the term “targeting agent” is meant to refer compoundswhich can be bound by and or react with other compounds. Targetingagents may be used to deliver chemotherapeutics, toxins, enzymes,radiotherapeutics, antibodies or imaging agents to cells that havetargeting agents associated with them and/or to convert or otherwisetransform or enhance co-administered active agents. A targeting agentmay include a moiety that constitutes a first agent that is localized tothe cell which when contacted with a second agent either is converted toa third agent which has a desired activity or causes the conversion ofthe second agent into an agent with a desired activity. The result isthe localized agent facilitates exposure of an agent with a desiredactivity to the metastasized cell.

As used herein, the term “radiosensitizing agent” is meant to refer toagents which increase the susceptibility of cells to the damagingeffects of ionizing radiation. A radiosensitizing agent permits lowerdoses of radiation to be administered and still provide atherapeutically effective dose.

As used herein, the term “imaging agent” is meant to refer to compoundswhich can be detected.

As used herein, the term “CRCA-1 translation product binding moiety” ismeant to refer to the portion of a conjugated compound that constitutesan CRCA-1 translation product ligand.

As used herein, the term “active moiety” is meant to refer to theportion of a conjugated compound that constitutes an active agent.

As used herein, the terms “conjugated compound” and “conjugatedcomposition” are used interchangeably and meant to refer to a compoundwhich comprises an CRCA-1 translation product binding moiety and anactive moiety and which is capable of binding to the CRCA-1 translationproduct. Conjugated compounds according to the present inventioncomprise a portion which constitutes an CRCA-1 translation productligand and a portion which constitutes an active agent. Thus, conjugatedcompounds according to the present invention are capable of specificallybinding to the CRCA-1 translation product and include a portion which isa therapeutic agent or imaging agent. Conjugated compositions maycomprise crosslinkers and/or molecules that serve as spacers between themoieties.

As used herein, the terms “crosslinker”, “crosslinking agent”,“conjugating agent”, “coupling agent”, “condensation reagent” and“bifunctional crosslinker” are used interchangeably and are meant torefer to molecular groups which are used to attach the CRCA-1translation product ligand and the active agent to thus form theconjugated compound.

As used herein, the term “colorectal cancer” is meant to include thewell-accepted medical definition that defines colorectal cancer as amedical condition characterized by cancer of cells of the intestinaltract below the small intestine (i.e. the large intestine (colon),including the cecum, ascending colon, transverse colon, descendingcolon, and sigmoid colon, and rectum). Additionally, as used herein, theterm “colorectal cancer” is meant to further include medical conditionswhich are characterized by cancer of cells of the duodenum and smallintestine (jejunum and ileum). The definition of colorectal cancer usedherein is more expansive than the common medical definition but isprovided as such since the cells of the duodenum and small intestinealso contain CRCA-1 translation products and are therefore amenable tothe methods of the present invention using the compounds of the presentinvention.

As used herein, the term “metastasis” is meant to refer to the processin which cancer cells originating in one organ or part of the bodyrelocate to another part of the body and continue to replicate.Metastasized cells subsequently form tumors which may furthermetastasize. Metastasis thus refers to the spread of cancer from thepart of the body where it originally occurs to other parts of the body.The present invention relates to methods of delivering active agents tometastasized colorectal cancer cells.

As used herein, the term “metastasized colorectal cancer cells” is meantto refer to colorectal cancer cells which have metastasized; colorectalcancer cells localized in a part of the body other than the duodenum,small intestine (jejunum and ileum), large intestine (colon), includingthe cecum, ascending colon, transverse colon, descending colon, andsigmoid colon, and rectum.

As used herein, the term “non-colorectal sample” and “extra-intestinalsample” are used interchangeably and meant to refer to a sample oftissue or body fluid from a source other than colorectal tissue. In somepreferred embodiments, the non-colorectal sample is a sample of tissuesuch as lymph nodes. In some preferred embodiments, the non-colorectalsample is a sample of extra-intestinal tissue which is an adenocarcinomaof unconfirmed origin. In some preferred embodiments, the non-colorectalsample is a blood sample.

As used herein, “an individual suffering from an adenocarcinoma ofunconfirmed origin” is meant to refer to an individual who has a tumorin which the origin has not been definitively identified.

As used herein, “an individual is suspected of being susceptible tometastasized colorectal cancer” is meant to refer to an individual whois at a particular risk of developing metastasized colorectal cancer.Examples of individuals at a particular risk of developing metastasizedcolorectal cancer are those whose family medical history indicates aboveaverage incidence of colorectal cancer among family members and/or thosewho have already developed colorectal cancer and have been effectivelytreated who therefore face a risk of relapse and recurrence.

As used herein, the term “antisense composition” and “antisensemolecules” are used interchangeably and are meant to refer to compoundsthat regulate transcription or translation by hybridizing to DNA or RNAand inhibiting and/or preventing transcription or translation fromtaking place. Antisense molecules include nucleic acid molecules andderivatives and analogs thereof. Antisense molecules hybridize to DNA orRNA in the same manner as complementary nucleotide sequences doregardless of whether or not the antisense molecule is a nucleic acidmolecule or a derivative or analog. Antisense molecules inhibit orprevent transcription or translation of genes whose expression is linkedto colorectal cancer.

As used herein, the term “CRCA-1 immunogen” is meant to refer to one ormore CRCA-1 translation products or a fragment thereof or a protein thatcomprises the same or a haptenized product thereof, cells and particleswhich display at least one CRCA-1 epitope, and haptenized cells andhaptenized particles which display at least one CRCA-1 epitope.

As used herein, the term “recombinant expression vector” is meant torefer to a plasmid, phage, viral particle or other vector which, whenintroduced into an appropriate host, contains the necessary geneticelements to direct expression of the coding sequence that encodes theprotein. The coding sequence is operably linked to the necessaryregulatory sequences. Expression vectors are well known and readilyavailable. Examples of expression vectors include plasmids, phages,viral vectors and other nucleic acid molecules or nucleic acid moleculecontaining vehicles useful to transform host cells and facilitateexpression of coding sequences.

ST Receptors and CRCA-1

Carcinomas derived from intestinal mucosa continue to express STreceptors on their cell surfaces. The expression of ST receptors bymetastatic tumors enables this protein and its mRNA to be a specificbiomarker for the presence of metastatic colorectal cancer cells inextra-intestinal tissues and blood. Indeed, this characteristic permitsthe detection of ST receptor mRNA by RT-PCR analysis to be a diagnostictest to stage patients with colorectal cancer and follow patients aftersurgery for evidence of recurrent disease in their blood. Further, theST receptor may be targeted with a ligand conjugated to an active agentin order to deliver the active agent to metastasized colotrectal tumorcells in vivo.

U.S. Pat. No. 5,518,888 issued May 21, 1996 to Waldman, PCT applicationPCT/US94/12232 filed Oct. 26, 1994, U.S. application Ser. No. 08/467,920filed Jun. 6, 1995, and U.S. application Ser. No. 08/583,447 filed Jan.5, 1996, which are each incorporated herein by reference, disclose thatmetastized colorectal tumors can be targetted for delivery of activecompounds by targetting ST receptors. The presence of ST receptors oncells outside fo the intestinal tract as a marker for colorectal cancerallows for the screening, identification and treatment of individualswith metastasized colorectal tumors. ST receptors may also be used totarget delivery of gene therapeutics and antisense compounds tocolorectal cells.

U.S. Pat. No. 5,601,990 issued Feb. 11, 1997, to Waldman, PCTapplication PCT/US94/12232 filed Oct. 26, 1994, and PCT applicationPCT/US97/07467 fileed May 2, 1997, which are each incorporated herein byreference, disclose that detection of evidence of expression of STreceptors in samples of tissue and body fluid from outside theintestinal tract indicate metastized colorectal cancer.

PCT application PCT/US97/07565 fileed May 2, 1997, which is incorporatedherein by reference, disclose that immunogens with epitopes that can betargetted by antibodies that react with ST receptors can be used invaccines compositions useful as prophylactic and therapeuticanti-metastatic colorectal cancer compositions.

Recently, studies have identified an alternative form of the mRNA forthe ST receptor, isolated from human colon carcinoma cells. This mRNAhas a substantial deletion of nucleic acids in the first exon in thecoding region of the ST receptor. This deletion results in a frameshiftof the coding region such that it no longer encodes the amino acidsequence of the ST receptor. However, this alternative splice variantmRNA appears to exhibit a selective pattern of expression that parallelsthat of the ST receptor. This newly-identified mRNA has been detectedonly in normal intestinal mucosal cells, human colorectal tumors, butnot in extra-intestinal tissues. Furthermore, the expression of thisnewly-identified mRNA can be detected by RT-PCR analysis separately fromST receptor mRNA. Thus, the present invention provides the use of thiscolorectal cancer-associated transcript (CRCA-1) as a specific moleculardiagnostic marker for the diagnosis, staging, and post-operativesurveillance of patients with colorectal cancer.

The newly-identified CRCA-1 appears to be a highly specific marker forthe diagnosis, staging, and post-operative surveillance of patients withcolorectal cancer. Detection of the expression of CRCA-1 employingmolecular techniques, including, but not limited to, RT-PCR, can beemployed to diagnose and stage patients, follow the development ofrecurrence after surgery, and, potentially, screen normal people for thedevelopment of colorectal cancer. Detection of the expression of CRCA-1employing molecular techniques, including, but not limited to, RT-PCR,can be employed to diagnose and stage patients, follow the developmentof recurrence after surgery, and, potentially, screen normal people forthe development of colorectal cancer.

The nucleotide sequence of the CRCA-1 transcription product is set forthas SEQ ID NO: 1. Cells of colorectal origin may be distinguished fromcells of other origin based by detecting the presence or absence of theCRCA-1 transcription product.

It has further been discovered that one or more translation products maybe produced from translation of the CRCA-1 transcription product. Thetranscription product contains a number of initiation codons from whichtranslation can begin, generating a number of translation products.Amino acid sequences of CRCA-1 translation products are set forth as SEQID NOs: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35,37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71,73, 75, 77, 79 and 81. Cells of colorectal origin may be distinguishedfrom cells of other origin by detecting the presence or absence of oneor more of the CRCA-1 translation products.

ST receptors are unique in that they are only localized in the apicalbrush border membranes of the cells lining the intestinal tract. Indeed,they are not found in any other cell type in placental mammals. Inaddition, ST receptors are almost exclusively localized to the apicalmembranes, with little being found in the basolateral membranes on thesides of intestinal cells. Like ST receptors, the expression of CRCA-1is similarly localized.

Mucosal cells lining the intestine are joined together by tightjunctions which form a barrier against the passage of intestinalcontents into the blood stream and components of the blood stream intothe intestinal lumen. Therefore, the apical location of cells expressingST receptors and CRCA-1 isolates results in the isolation of such cellsfrom the circulatory system so that they may be considered to existseparate from the rest of the body; essentially the “outside” of thebody. Therefore, the rest of the body is considered “outside” theintestinal tract. Compositions administered “outside” the intestinaltract are maintained apart and segregated from the only cells whichnormally express ST receptors. Conversely, tissue samples taken fromtissue outside of the intestinal tract do not normally contain cellswhich express ST receptors and CRCA-1.

In individuals suffering from colorectal cancer, the cancer cells areoften derived from cells that produce and display the ST receptor andthese cancer cells continue to produce and display the ST receptor ontheir cell surfaces. It has been observed that CRCA-1 is expressed bycolorectal cancer cells.

When such cancer cells metastasize, the metastasized cancer cellscontinue to produce and display the ST receptor. The expression ofCRCA-1 by metastatic tumor cells provides a detectable target for invitro screening, diagnosis, monitoring and staging as well as a targetfor in vivo delivery of conjugated compositions that comprise activeagents for the imaging and treatment.

The present invention relates to isolated CRCA-1 translation products.The present invention relates to isolated CRCA-1 transcript. The presentinvention relates to isolated antibodies specific for such products andto hybridomas which produce such antibodies. Isolated translationproducts or functional fragments thereof are useful to genrate antibodesaccording to the invention. Some aspects of the invention nucleic acidmolecules that encode the translation products. Nucleic acid moleculesare useful to produce proteins which are be used to generate antibodies.

The present invention provides an isolated nucleic molecule thatcomprises a nucleic acid sequence that encodes a protein having an aminoacid sequence which comprises SEQ ID NO:3. In some such embodiments, thenucleic molecule comprises SEQ ID NO:2. In some embodiments, arecombinant expression vector comprises such nucleic acid molecules anda host cell may comprise such recombinant expression vector.

The present invention provides an isolated nucleic acid molecule havinga nucleic acid sequence of SEQ ID NO:1 or a fragment thereof consistingof 10 or more nucleotides including nucleotides 110–113 of SEQ ID NO:1.According to some embodiments, such nucleic acid molecules have anucleic acid sequence of SEQ ID NO:1 or SEQ ID NO:2. In someembodiments, a recombinant expression vector comprises such nucleic acidmolecules and a host cell may comprise such recombinant expressionvector. In some embodiments, such nucleic acid molecule consists of12–150 nucleotides of SEQ ID NO:1. In some embodiments, such nucleicacid molecule consists of 15–50 nucleotides of SEQ ID NO:1.

The present invention provides an isolated oligonucleotide moleculeconsisting of a nucleotide sequence complementary to a fragment of SEQID NO:1, said fragment consisting of 5 or more nucleotides includingnucleotides 110–113 of SEQ ID NO:1. In some embodiments, such isolatedoligonucleotide molecules consist of 5–50 nucleotides. In someembodiments, such isolated oligonucleotide molecules consist of 10–40nucleotides. In some embodiments, such isolated oligonucleotidemolecules consist of 15–25 nucleotides. In some embodiments, suchisolated oligonucleotide molecules consist of 10–150 nucleotides. Insome embodiments, such isolated oligonucleotide molecules consist of18–28 nucleotides. In some embodiments, such isolated oligonucleotidemolecules consist of 10 or more nucleotides.

In vitro Diagnostics

According to some embodiments of the invention, compositions, kits andin vitro methods are provided for screening, diagnosiing and analyzingpatients and patient samples to detect evidence of CRCA-1 expression bycells outside of the intestinal tract wherein the expression of CRCA-1is indicative of metastasis of colorectal cancer. Furthermore, thepresent invention relates to methods, compositions and kits useful inthe in vitro screening, diagnosis and analysis of patient and patientsamples to detect evidence of CRCA-1 expression by tumor cells outsideof the intestinal tract wherein the presence of cells that expressCRCA-1 indicates and/or confirms that a tumor is of colorectal cancerorigin. In an additional aspect of the invention, compositions, kits andmethods are provided which are useful to visualize colorectal cells.Such compositions, kits and methods of analyzing tissue samples from thecolon tissue to evaluate the extent of metastasis or invasion ofcolorectal tumor cells into the lamina propria.

In vitro screening and diagnostic compositions, methods and kits can beused in the monitoring of individuals who are in high risk groups forcolorectal cancer such as those who have been diagnosed with localizeddisease and/or metastasized disease and/or those who are geneticallylinked to the disease. In vitro screening and diagnostic compositions,methods and kits can be used in the monitoring of individuals who areundergoing and/or have been treated for localized colorectal cancer todetermine if the cancer has metastasized. In vitro screening anddiagnostic compositions, methods and kits can be used in the monitoringof individuals who are undergoing and/or have been treated formetastasized colorectal cancer to determine if the metastasized cancerhas been eliminated. In vitro screening and diagnostic compositions,methods and kits can be used in the monitoring of individuals who areotherwise susceptible, i.e. individuals who have been identified asgenetically predisposed such as by genetic screening and/or familyhistories. Advancements in the understanding of genetics anddevelopments in technology as well as epidemiology allow for thedetermination of probability and risk assessment an individual has fordeveloping colorectal cancer. Using family health histories and/orgenetic screening, it is possible to estimate the probability that aparticular individual has for developing certain types of cancerincluding colorectal cancer. Those individuals that have been identifiedas being predisposed to developing a particular form of cancer can bemonitored or screened to detect evidence of metastasized colorectalcancer. Upon discovery of such evidence, early treatment can beundertaken to combat the disease. Accordingly, individuals who are atrisk for developing metastasized colorectal cancer may be identified andsamples may be isolated form such individuals. The invention isparticularly useful for monitoring individuals who have been identifiedas having family medical histories which include relatives who havesuffered from colorectal cancer. Likewise, the invention is particularlyuseful to monitor individuals who have been diagnosed as havingcolorectal cancer and, particularly those who have been treated and hadtumors removed and/or are otherwise experiencing remission includingthose who have been treated for metastasized colorectal cancer.

In vitro screening and diagnostic compositions, methods and kits can beused in the analysis of tumors. Expression of CRCA-1 is a marker forcell type and allows for the identification of the origin ofadenocarcinoma of unconfirmed origin as colorectal tumors as well asallowing for an initial diagnosis of colorectal cancer to be confirmed.Tumors believed to be colorectal in origin can be confirmed as suchusing the compositions, methods and kits of the invention. The inventioncan be used to confirm the diagnosis of colorectal cancer by confirmingthat tumors are of colorectal origin. Similarly, tumors of unknownorigin can be analyzed and identified as being colorectal in originusing the compositions, methods and kits of the invention. The inventioncan be used to identify colorectal tumors in samples of tumors removedfrom individuals suffering from adenocarcinomas of unconfirmed origin.

In vitro screening and diagnostic compositions, kits and methods of theinvention can be used to analyze tissue samples from the colon tissue toevaluate the extent of metastasis or invasion of colorectal tumor cellsinto the lamina propria. The lamina propria represents the barrierbetween the colorectal tract and the rest of the body; see Bailey'sTextbook of Histology, 16th edition, Coperhaven et al. 1975 Williams andWilkens, Baltimore Md. at page 404 which is incorporated herein byreference. By identifying the presence of CRCA-1 transcript ortranslation products in cells of the lamina propria, the extent ofinvasion/infiltration of colorectal tumor cells into non-colorectaltissue can be evaluated and confirmed.

According to the invention, compounds are provided which bind to CRCA-1transcript or translation products. Normal tissue in the body does nothave CRCA-1 transcript or translation products except cells of theintestinal tract. Metastasized colorectal cells may be identified bydetecting in non-colorectal samples CRCA-1 transcript or translationproducts. The expression of CRCA-1 is a marker for cell type and allowsfor the identification of colorectal metastasis in extra-intestinalsamples. CRCA-1 transcript or translation products may be used tovisualize colorectal derived cells from other cells of the lumen inorder to evaluate the level of invasion of colorectal tumor cells intothe basement membrane.

In some embodiments of the invention, non-colorectal tissue and fluidsamples or tumor samples may be screened to identify the presence orabsence of CRCA-1 translation products. Techniques such as ELISA assaysand Western blots may be performed to determine whether one or moreCRCA-1 translation products are present in a sample.

In some embodiments of the invention, non-colorectal tissue and fluidsamples or tumor samples may be screened to identify whether one or moreCRCA-1 translation products are being expressed in cells outside of thecolorectal tract by detecting the presence or absence of CRCA-1transcript. The presence of CRCA-1 transcript or cDNA generatedtherefrom can be determined using techniques such as PCR amplification,branched oligonucleotide technology, Northern Blots (mRNA), SouthernBlots (cDNA), or oligonucleotide hybridization.

In some embodiments of the invention, cells of non-colorectal tissuesamples or tumor samples may be examined to identify the presence orabsence of one or more CRCA-1 translation products. Techniques such asimmunohistochemistry blots may be performed on tissue sections todetermine whether one or more CRCA-1 translation products are present ina sample.

In some embodiments of the invention, cells of non-colorectal tissuesamples or tumor samples may be examined to determine whether one ormore CRCA-1 translation products is being expressed in cells outside ofthe colorectal tract by detecting the presence or absence of the CRCA-1transcript. The presence of the CRCA-1 transcript or cDNA generatedtherefrom in cells from tissue sections can be determined usingtechniques such as in situ hybridization.

The presence of one or more CRCA-1 translation products innon-colorectal tissue and fluid samples or on cells from non-colorectaltissue samples indicates colorectal tumor metastasis. The presence ofone or more CRCA-1 translation products in a tumor sample or on tumorcells indicates that the tumor is colorectal in origin. The presence ofthe CRCA-1 transcript in non-colorectal tissue and fluid samples or incells from non-colorectal tissue samples indicates colorectal tumormetastasis. The presence of the CRCA-1 transcript in tumor samples andtumor cells indicates that the tumor is colorectal in origin.

Some aspects of the present invention relate to methods and kits forevaluating the metastatic migration of tumor cells in the laminapropria, indicating the level of invasion of colorectal tumor cells intothe basement membrane. In some embodiments of the invention, tissuesamples which include sections of the lamina propria may be isolatedfrom individuals undergoing or recovery from surgery to removecolorectal tumors. The tissue is analyzed to determine the extent ofinvasion into the basement membrane of the lamina propria by neoplasticcolorectal cells. Identification of the presence or absence of the oneor more CRCA-1 translation products confirms evaluation of the migrationof tumor cells into the basement membrane indicating metastasis.Techniques such as immunohistochemistry assays may be performed todetermine whether one or more CRCA-1 translation products are present incells in the tissue sample which are indicative of metastatic migration.Alternatively, in some embodiments of the invention, tissue samples thatinclude the lamina propria are analyzed to identify whether one or moreCRCA-1 translation products are being expressed in cells in the tissuesample which indicate metastatic migration by detecting the presence orabsence of the CRCA-1 transcript. The presence of the CRCA-1 transcriptor cDNA generated therefrom can be determined using techniques such asin situ hybridization.

Samples from tumors may be identified as colorectal in origin byidentification of expression of one or more CRCA-1 translation productsusing the methods of the invention. Samples of tumors removed fromindividuals suffering from adenocarcinomas of unconfirmed origin can betested to determine whether or not they possess one or more CRCA-1translation products or the CRCA-1 transcript. If the sample is removedfrom the intestinal tract, a section of frozen cells can be examined todetermine if the tumor cells express one or more CRCA-1 translationproducts. If the sample is removed from the extra-intestinal tissue, asection of frozen cells can be examined to determine if the tumor cellsexpress one or more CRCA-1 translation products or the sample can behomogenized and tested since the non-cancer cells will not possess oneor more CRCA-1 translation products and therefore not presentbackground.

Samples may be obtained from resected tissue or biopsy materialincluding needle biopsy. Tissue section preparation for surgicalpathology may be frozen and prepared using standard techniques.Immunohistochemistry and in situ hybridization binding assays on tissuesections are performed in fixed cells. Extra-intestinal samples may behomogenized by standard techniques such as sonication, mechanicaldisruption or chemical lysis such as detergent lysis. It is alsocontemplated that tumor samples in body such as blood, urine, lymphfluid, cerebral spinal fluid, amniotic fluid, vaginal fluid, semen andstool samples may also be screened to determine if such tumors arecolorectal in origin.

Non-colorectal tissue samples may be obtained from any tissue exceptthose of the colorectal tract, i.e. the intestinal tract below the smallintestine (i.e. the large intestine (colon), including the cecum,ascending colon, transverse colon, descending colon, and sigmoid colon,and rectum) and additionally the duodenum and small intestine (jejunumand ileum). The cells of all tissue except those of the colorectal tractdo not express one or more CRCA-1 translation products. Thus if one ormore CRCA-1 translation products or the CRCA-1 transcript are detectedin non-colorectal samples, the presence of metastatic colorectal cancercells is indicated. In some preferred embodiments, the tissue samplesare lymph nodes.

Tissue samples may be obtained by standard surgical techniques includinguse of biopsy needles. One skilled in the art would readily appreciatethe variety of test samples that may be examined for one or more CRCA-1translation products and recognize methods of obtaining tissue samples.

Tissue samples may be homogenized or otherwise prepared for screeningfor the presence of one or more CRCA-1 translation products by wellknown techniques such as sonication, mechanical disruption, chemicallysis such as detergent lysis or combinations thereof.

Examples of body fluid samples include blood, urine, lymph fluid,cerebral spinal fluid, amniotic fluid, vaginal fluid and semen. In somepreferred embodiments, blood is used as a sample of body fluid. Cellsmay be isolated from fluid sample such as centrifugation. One skilled inthe art would readily appreciate the variety of test samples that may beexamined for one or more CRCA-1 translation products. Test samples maybe obtained by such methods as withdrawing fluid with a syringe or by aswab. One skilled in the art would readily recognize other methods ofobtaining test samples.

In an assay using a blood sample, the blood plasma may be separated fromthe blood cells. The blood plasma may be screened for one or more CRCA-1translation products including truncated proteins which are releasedinto the blood when one or more CRCA-1 translation products are cleavedfrom or sloughed off from metastasized colorectal tumor cells. In someembodiments, blood cell fractions are screened for the presence ofmetastasized colorectal tumor cells. In some embodiments, lymphocytespresent in the blood cell fraction are screened by lysing the cells anddetecting the presence of one or more CRCA-1 translation products or theCRCA-1 transcript which may be present as a result of the presence ofany metastasized colorectal tumor cells that may have been engulfed bythe blood cell.

For aspects of the invention related to analysis of lumen tissue, theinvention is useful to evaluate the level of metastatic migration ofcolorectal tumor cells using lumen samples taken from surgery patientsat and near the site of the tumor. Some aspects of the invention providemethods of analyzing tissue samples which are fixed sections routinelyprepared by surgical pathologists to characterize and evaluate cells. Insome embodiments, the cells are from lamina propria and are analyzed todetermine and evaluate the extent of metastasis of colorectal tumorcells. The lamina propria represents the barrier between the colorectaltract and the rest of the body. By identifying the presence of theCRCA-1 transcript or one or more CRCA-1 translation products in cells ofthe lamina propria, the extent of invasion/infiltration of colorectaltumor cells into non-colorectal tissue can be evaluated. In someembodiments, the cells are removed in a biopsy or as an adenocarcinomaof unknown origin and are analyzed to determine and evaluate the whetherthey are colorectal tumor cells. In some embodiments, the cells are froma tumor suspected of being colorectal in origin and the method andcompositions and kits of the invention are used to confirm the identityof the origin of the tumor cells.

Samples of the lamina propria are removed during colorectal tumorremoval surgery such as by resection or colonoscopy. The sampleincluding basement membrane cells is frozen. If immunohistochemistry orin situ hybridization is to be performed, the frozen section is stainedand then the assay is run. Those having ordinary skill in the art canreadily isolate samples which include portions of the lamina propria andfix and stain them using standard techniques. By adding thevisualization provided with a CRCA-1 detection technique, the sectioncan be more comprehensively analyzed and the level of invasion ofneoplastic colorectal cells into the lamina propria can be determined.The present invention may be used to analyze and evaluate the extent ofprogression of localized colorectal tumors, that is primary ornon-metastatic colorectal tumors if these have penetrated the basementmembrane underlying the mucosa into the submucosa.

Immunoassay methods may be used to identify individuals suffering fromcolorectal cancer metastasis by detecting presence of one or more CRCA-1translation products in sample of non-colorectal tissue or body fluidusing antibodies which were produced in response to exposure to suchCRCA-1 translation product. Moreover, immunoassay methods may be used toidentify individuals suffering from colorectal cancer by detectingpresence of one or more CRCA-1 translation products in sample of tumorusing antibodies which were produced in response to exposure to suchCRCA-1 translation product.

The antibodies are preferably monoclonal antibodies. The antibodies arepreferably raised against one or more CRCA-1 translation products madein human cells. Immunoassays are well known and there design may beroutinely undertaken by those having ordinary skill in the art. Thosehaving ordinary skill in the art can produce monoclonal antibodies whichspecifically bind to one of the several CRCA-1 translation products andare useful in methods and kits of the invention using standardtechniques and readily available starting materials. The techniques forproducing monoclonal antibodies are outlined in Harlow, E. and D. Lane,(1988) ANTIBODIES: A Laboratory Manual, Cold Spring Harbor Laboratory,Cold Spring Harbor N.Y., which is incorporated herein by reference,provide detailed guidance for the production of hybridomas andmonoclonal antibodies which specifically bind to target proteins. It iswithin the scope of the present invention to include FAbs and F(Ab)2swhich specifically bind to one or more CRCA-1 translation products inplace of antibodies.

Briefly, a CRCA-1 translation product is injected into mice. The spleenof the mouse is removed, the spleen cells are isolated and fused withimmortalized mouse cells. The hybrid cells, or hybridomas, are culturedand those cells which secrete antibodies are selected. The antibodiesare analyzed and, if found to specifically bind to the CRCA-1translation product, the hybridoma which produces them is cultured toproduce a continuous supply of anti-CRCA-1 translation product specificantibodies.

The present invention relates to antibodies which are produced inresponse to exposure to a CRCA-1 translation product. The antibodies arepreferably monoclonal antibodies. The antibodies are preferably raisedagainst CRCA-1 translation product made in human cells.

The means to detect the presence of a protein in a test sample areroutine and one having ordinary skill in the art can detect the presenceor absence of a protein or an antibody using well known methods. Onewell known method of detecting the presence of a protein is animmunoassay. One having ordinary skill in the art can readily appreciatethe multitude of ways to practice an immunoassay to detect the presenceof a CRCA-1 translation product in a sample.

According to some embodiments, immunoassays comprise allowing proteinsin the sample to bind a solid phase support such as a plastic surface.Detectable antibodies are then added which selectively binding to eitherthe CRCA-1 translation product. Detection of the detectable antibodyindicates the presence of CRCA-1 translation product. The detectableantibody may be a labelled or an unlabelled antibody. Unlabelledantibody may be detected using a second, labelled antibody thatspecifically binds to the first antibody or a second, unlabelledantibody which can be detected using labelled protein A, a protein thatcomplexes with antibodies. Various immunoassay procedures are describedin Immunoassays for the 80's, A. Voller et al., Eds., University Park,1981, which is incorporated herein by reference.

Simple immunoassays may be performed in which a solid phase support iscontacted with the test sample. Any proteins present in the test samplebind the solid phase support and can be detected by a specific,detectable antibody preparation. Such a technique is the essence of thedot blot, Western blot and other such similar assays.

Other immunoassays may be more complicated but actually provideexcellent results. Typical and preferred immunometric assays include“forward” assays for the detection of a protein in which a firstanti-protein antibody bound to a solid phase support is contacted withthe test sample. After a suitable incubation period, the solid phasesupport is washed to remove unbound protein. A second, distinctanti-protein antibody is then added which is specific for a portion ofthe specific protein not recognized by the first antibody. The secondantibody is preferably detectable. After a second incubation period topermit the detectable antibody to complex with the specific proteinbound to the solid phase support through the first antibody, the solidphase support is washed a second time to remove the unbound detectableantibody. Alternatively, the second antibody may not be detectable. Inthis case, a third detectable antibody, which binds the second antibodyis added to the system. This type of “forward sandwich” assay may be asimple yes/no assay to determine whether binding has occurred or may bemade quantitative by comparing the amount of detectable antibody withthat obtained in a control. Such “two-site” or “sandwich” assays aredescribed by Wide, Radioimmune Assay Method, Kirkham, Ed., E. & S.Livingstone, Edinburgh, 1970, pp. 199–206, which is incorporated hereinby reference.

Other types of immunometric assays are the so-called “simultaneous” and“reverse” assays. A simultaneous assay involves a single incubation stepwherein the first antibody bound to the solid phase support, the second,detectable antibody and the test sample are added at the same time.After the incubation is completed, the solid phase support is washed toremove unbound proteins. The presence of detectable antibody associatedwith the solid support is then determined as it would be in aconventional “forward sandwich” assay. The simultaneous assay may alsobe adapted in a similar manner for the detection of antibodies in a testsample.

The “reverse” assay comprises the stepwise addition of a solution ofdetectable antibody to the test sample followed by an incubation periodand the addition of antibody bound to a solid phase support after anadditional incubation period. The solid phase support is washed inconventional fashion to remove unbound protein/antibody complexes andunreacted detectable antibody. The determination of detectable antibodyassociated with the solid phase support is then determined as in the“simultaneous” and “forward” assays. The reverse assay may also beadapted in a similar manner for the detection of antibodies in a testsample.

The first component of the immunometric assay may be added tonitrocellulose or other solid phase support which is capable ofimmobilizing proteins. The first component for determining the presenceof CRCA-1 translation product in a test sample is an anti-CRCA-1translation product antibody. By “solid phase support” or “support” isintended any material capable of binding proteins. Well-known solidphase supports include glass, polystyrene, polypropylene, polyethylene,dextran, nylon, amylases, natural and modified celluloses,polyacrylamides, agaroses, and magnetite. The nature of the support canbe either soluble to some extent or insoluble for the purposes of thepresent invention. The support configuration may be spherical, as in abead, or cylindrical, as in the inside surface of a test tube or theexternal surface of a rod. Alternatively, the surface may be flat suchas a sheet, test strip, etc. Those skilled in the art will know manyother suitable “solid phase supports” for binding proteins or will beable to ascertain the same by use of routine experimentation. Apreferred solid phase support is a 96-well microtiter plate.

To detect the presence of one or more CRCA-1 translation products,detectable anti-CRCA-1 translation product antibodies are used. Severalmethods are well known for the detection of antibodies.

One method in which the antibodies can be detectably labelled is bylinking the antibodies to an enzyme and subsequently using theantibodies in an enzyme immunoassay (EIA) or enzyme-linked immunosorbentassay (ELISA), such as a capture ELISA. The enzyme, when subsequentlyexposed to its substrate, reacts with the substrate and generates achemical moiety which can be detected, for example, byspectrophotometric, fluorometric or visual means. Enzymes which can beused to detectably label antibodies include, but are not limited tomalate dehydrogenase, staphylococcal nuclease, delta-5-steroidisomerase, yeast alcohol dehydrogenase, alpha-glycerophosphatedehydrogenase, triose phosphate isomerase, horseradish peroxidase,alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase,ribonuclease, urease, catalase, glucose-6-phosphate dehydrogenase,glucoamylase and acetylcholinesterase. One skilled in the art wouldreadily recognize other enzymes which may also be used.

Another method in which antibodies can be detectably labelled is throughradioactive isotopes and subsequent use in a radioimmunoassay (RIA)(see, for example, Work, T. S. et al., Laboratory Techniques andBiochemistry in Molecular Biology, North Holland Publishing Company,N.Y., 1978, which is incorporated herein by reference). The radioactiveisotope can be detected by such means as the use of a gamma counter or ascintillation counter or by autoradiography. Isotopes which areparticularly useful for the purpose of the present invention are ³H,¹²⁵I, ¹³¹I, ³⁵S, and ¹⁴C. Preferably ¹²⁵I is the isotope. One skilled inthe art would readily recognize other radioisotopes which may also beused.

It is also possible to label the antibody with a fluorescent compound.When the fluorescent-labelled antibody is exposed to light of the properwave length, its presence can be detected due to its fluorescence. Amongthe most commonly used fluorescent labeling compounds are fluoresceinisothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin,o-phthaldehyde and fluorescamine. One skilled in the art would readilyrecognize other fluorescent compounds which may also be used.

Antibodies can also be detectably labelled using fluorescence-emittingmetals such as ¹⁵²Eu, or others of the lanthanide series. These metalscan be attached to the protein-specific antibody using such metalchelating groups as diethylenetriaminepentaacetic acid (DTPA) orethylenediamine-tetraacetic acid (EDTA). One skilled in the art wouldreadily recognize other fluorescence-emitting metals as well as othermetal chelating groups which may also be used.

Antibody can also be detectably labelled by coupling to achemiluminescent compound. The presence of the chemiluminescent-labelledantibody is determined by detecting the presence of luminescence thatarises during the course of a chemical reaction. Examples ofparticularly useful chemoluminescent labeling compounds are luminol,isoluminol, theromatic acridinium ester, imidazole, acridinium salt andoxalate ester. One skilled in the art would readily recognize otherchemiluminescent compounds which may also be used.

Likewise, a bioluminescent compound may be used to label antibodies.Bioluminescence is a type of chemiluminescence found in biologicalsystems in which a catalytic protein increases the efficiency of thechemiluminescent reaction. The presence of a bioluminescent protein isdetermined by detecting the presence of luminescence. Importantbioluminescent compounds for purposes of labeling are luciferin,luciferase and aequorin. One skilled in the art would readily recognizeother bioluminescent compounds which may also be used.

Detection of the protein-specific antibody, fragment or derivative maybe accomplished by a scintillation counter if, for example, thedetectable label is a radioactive gamma emitter. Alternatively,detection may be accomplished by a fluorometer if, for example, thelabel is a fluorescent material. In the case of an enzyme label, thedetection can be accomplished by colorometric methods which employ asubstrate for the enzyme. Detection may also be accomplished by visualcomparison of the extent of enzymatic reaction of a substrate incomparison with similarly prepared standards. One skilled in the artwould readily recognize other appropriate methods of detection which mayalso be used.

The binding activity of a given lot of antibodies may be determinedaccording to well known methods. Those skilled in the art will be ableto determine operative and optimal assay conditions for eachdetermination by employing routine experimentation.

Positive and negative controls may be performed in which known amountsof one or more CRCA-1 translation products and no CRCA-1 translationproduct, respectively, are added to assays being performed in parallelwith the test assay. One skilled in the art would have the necessaryknowledge to perform the appropriate controls. In addition, the kit maycomprise instructions for performing the assay. Additionally the kit mayoptionally comprise depictions or photographs that represent theappearence of positive and negative results.

CRCA-1 translation products may be produced as a reagent for positivecontrols routinely. One skilled in the art would appreciate thedifferent manners in which the CRCA-1 translation products may beproduced and isolated.

Antibody composition refers to the antibody or antibodies required forthe detection of the protein. For example, the antibody composition usedfor the detection of a CRCA-1 translation product in a test samplecomprises a first antibody that binds to the CRCA-1 translation productas well as a second or third detectable antibody that binds the first orsecond antibody, respectively.

To examine a test sample for the presence of a CRCA-1 translationproduct, a standard immunometric assay such as the one described belowmay be performed. A first anti-CRCA-1 translation product antibody,which recognizes a specific portion of CRCA-1 translation product, isadded to a 96-well microtiter plate in a volume of buffer. The plate isincubated for a period of time sufficient for binding to occur andsubsequently washed with PBS to remove unbound antibody. The plate isthen blocked with a PBS/BSA solution to prevent sample proteins fromnon-specifically binding the microtiter plate. Test sample aresubsequently added to the wells and the plate is incubated for a periodof time sufficient for binding to occur. The wells are washed with PBSto remove unbound protein. Labelled anti-CRCA-1 translation productantibodies, which recognize portions of CRCA-1 translation product notrecognized by the first antibody, are added to the wells. The plate isincubated for a period of time sufficient for binding to occur andsubsequently washed with PBS to remove unbound, labelled anti-CRCA-1translation product antibody. The amount of labelled and boundanti-CRCA-1 translation product antibody is subsequently determined bystandard techniques.

Kits which are useful for the detection of a CRCA-1 translation productin a test sample comprise a container comprising anti-CRCA-1 translationproduct antibodies and a container or containers comprising controls.Controls include one control sample which does not contain CRCA-1translation product and/or another control sample which contained theCRCA-1 translation product. The anti-CRCA-1 translation productantibodies used in the kit are detectable such as being detectablylabelled. If the detectable anti-CRCA-1 translation product antibody isnot labelled, it may be detected by second antibodies or protein A forexample which may also be provided in some kits in separate containers.Additional components in some kits include solid support, buffer, andinstructions for carrying out the assay. Additionally the kit mayoptionally comprise depictions or photographs that represent theappearence of positive and negative results.

The immunoassay is useful for detecting one or more CRCA-1 translationproducts in homogenized tissue samples and body fluid samples includingthe plasma portion or cells in the fluid sample.

Western Blots may be used in methods of identifying individualssuffering from colorectal cancer metastasis by detecting presence of oneor more CRCA-1 translation products of non-colorectal tissue or bodyfluid. Western blots may also be used to detect presence of one or moreCRCA-1 translation products in sample of tumor from an individualsuffering from cancer to identify and/or confirm that the tumor iscolorectal in origin. Western blots use detectable anti-CRCA-1translation product antibodies to bind to any CRCA-1 translation productpresent in a sample and thus indicate the presence of the receptor inthe sample.

Western blot techniques, which are described in Sambrook, J. et al.,(1989) Molecular Cloning: A Laboratory Manual, Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., which is incorporated hereinby reference, are similar to immunoassays with the essential differencebeing that prior to exposing the sample to the antibodies, the proteinsin the samples are separated by gel electrophoresis and the separatedproteins are then probed with antibodies. In some preferred embodiments,the matrix is an SDS-PAGE gel matrix and the separated proteins in thematrix are transferred to a carrier such as filter paper prior toprobing with antibodies. Anti-CRCA-1 translation product antibodiesdescribed above are useful in Western blot methods.

Generally, samples are homogenized and cells are lysed using detergentsuch as Triton-X. The material is then separated by the standardtechniques in Sambrook, J. et al., (1989) Molecular Cloning: ALaboratory Manual, Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y.

Kits which are useful for the detection of one or more CRCA-1translation products in a test sample by Western Blot comprise acontainer comprising anti-CRCA-1 translation products antibodies and acontainer or containers comprising controls. Controls include onecontrol sample which does not contain CRCA-1 translation product and/oranother control sample which contained one or more CRCA-1 translationproducts. The anti-CRCA-1 translation product antibodies used in the kitare detectable such as being detectably labelled. If the detectableanti-CRCA-1 translation product antibody is not labelled, it may bedetected by second antibodies or protein A for example which may also beprovided in some kits in separate containers. Additional components insome kits include instructions for carrying out the assay. Additionallythe kit may optionally comprise depictions or photographs that representthe appearence of positive and negative results.

Western blots are useful for detecting one or more CRCA-1 translationproducts in homogenized tissue samples and body fluid samples includingthe plasma portion or cells in the fluid sample.

In addition to detection of one or more CRCA-1 translation products,aspects of the present invention include various methods of determiningwhether a sample contains cells that express CRCA-1 by nucleotidesequence-based molecular analysis to detect the CRCA-1 transcript.Several different methods are available for doing so including thoseusing Polymerase Chain Reaction (PCR) technology, branchedoligonucleotide technology, Northern blot technology, oligonucleotidehybridization technology, and in situ hybridization technology.

The invention relates to oligonucleotide probes and primers used in themethods of identifying the CRCA-1 transcript and to diagnostic kitswhich comprise such components. The mRNA sequence-based methods fordetect the CRCA-1 transcript include but are not limited to polymerasechain reaction technology, branched oligonucleotide technology, Northernand Southern blot technology, in situ hybridization technology andoligonucleotide hybridization technology.

The methods described herein are meant to exemplify how the presentinvention may be practiced and are not meant to limit the scope ofinvention. It is contemplated that other sequence-based methodology fordetecting the presence of the CRCA-1 transcript in non-colorectalsamples may be employed according to the invention.

A preferred method to detecting the CRCA-1 transcript in geneticmaterial derived from non-colorectal samples uses polymerase chainreaction (PCR) technology. PCR technology is practiced routinely bythose having ordinary skill in the art and its uses in diagnostics arewell known and accepted. Methods for practicing PCR technology aredisclosed in “PCR Protocols: A Guide to Methods and Applications”,Innis, M. A., et al. Eds. Academic Press, Inc. San Diego, Calif. (1990)which is incorporated herein by reference. Applications of PCRtechnology are disclosed in “Polymerase Chain Reaction” Erlich, H. A.,et al., Eds. Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989)which is incorporated herein by reference. U.S. Pat. No. 4,683,202, U.S.Pat. No. 4,683,195, U.S. Pat. No. 4,965,188 and U.S. Pat. No. 5,075,216,which are each incorporated herein by reference describe methods ofperforming PCR. PCR may be routinely practiced using Perkin Elmer CetusGENE AMP RNA PCR kit, Part No. N808-0017.

PCR technology allows for the rapid generation of multiple copies of DNAsequences by providing 5′ and 3′ primers that hybridize to sequencespresent in an RNA or DNA molecule, and further providing freenucleotides and an enzyme which fills in the complementary bases to thenucleotide sequence between the primers with the free nucleotides toproduce a complementary strand of DNA. The enzyme will fill in thecomplementary sequences adjacent to the primers. If both the 5′ primerand 3′ primer hybridize to nucleotide sequences on the same smallfragment of nucleic acid, exponential amplification of a specificdouble-stranded size product results. If only a single primer hybridizesto the nucleic acid fragment, linear amplification producessingle-stranded products of variable length.

PCR primers can be designed routinely by those having ordinary skill inthe art using sequence information. The nucleotide sequence of the theCRCA-1 transcript is set forth in SEQ ID NO:1. To perform this method,RNA is extracted from cells in a sample and tested or used to make cDNAusing well known methods and readily available starting materials. Thosehaving ordinary skill in the art can readily prepare PCR primers. A setof primers generally contains two primers. When performing PCR onextracted mRNA or cDNA generated therefrom, if the CRCA-1 transcript orcDNA generated thererefrom is present, multiple copies of the mRNA orcDNA will be made. If it is not present, PCR will not generate adiscrete detectable product. Primers are generally 8–50 nucleotides,preferably about 15–35 nucleotides, more preferably 18–28 nucleotides,which are identical or complementary to and therefor hybridize to theCRCA-1 transcript or cDNA generated therefrom. In preferred embodiments,the primers are each 15–35 nucleotide, more preferably 18–28 nucleotidefragments of SEQ ID NO:1. The primer must hybridize to the sequence tobe amplified. Typical primers are 18–28 nucleotides in length and aregenerally have 50% to 60% G+C composition. The entire primer ispreferably complementary to the sequence it must hybridize to.Preferably, primers generate PCR products 100 base pairs to 2000 basepairs. However, it is possible to generate products of 50 to up to 10 kband more. If mRNA is used as a template, the primers must hybridize tomRNA sequences. If cDNA is used as a template, the primers musthybridize to cDNA sequences. At least one primer hybridizes to a uniquenucleotide sequence not found on mRNA that encodes ST receptor protein.

The mRNA or cDNA is combined with the primers, free nucleotides andenzyme following standard PCR protocols. The mixture undergoes a seriesof temperature changes. If the CRCA-1 transcript or cDNA generatedtherefrom is present, that is, if both primers hybridize to sequences onthe same molecule, the molecule comprising the primers and theintervening complementary sequences will be exponentially amplified. Theamplified DNA can be easily detected by a variety of well known means.If no CRCA-1 transcript or cDNA generated therefrom is present, no PCRproduct will be exponentially amplified. The PCR technology thereforeprovides an extremely easy, straightforward and reliable method ofdetecting the CRCA-1 transcript in a sample.

PCR product may be detected by several well known means. The preferredmethod for detecting the presence of amplified DNA is to separate thePCR reaction material by gel electrophoresis and stain the gel withethidium bromide in order to visual the amplified DNA if present. A sizestandard of the expected size of the amplified DNA is preferably run onthe gel as a control.

In some instances, such as when unusually small amounts of RNA arerecovered and only small amounts of cDNA are generated therefrom, it isdesirable or necessary to perform a PCR reaction on the first PCRreaction product. That is, if difficult to detect quantities ofamplified DNA are produced by the first reaction, a second PCR can beperformed to make multiple copies of DNA sequences of the firstamplified DNA. A nested set of primers are used in the second PCRreaction. The nested set of primers hybridize to sequences downstream ofthe 5′ primer and upstream of the 3′ primer used in the first reaction.

The present invention includes oligonucleotide which are useful asprimers for performing PCR methods to amplify the CRCA-1 transcript orcDNA generated therefrom.

According to the invention, diagnostic kits can be assembled which areuseful to practice methods of detecting the presence of the CRCA-1transcript or cDNA generated therefrom in non-colorectal samples. Suchdiagnostic kits comprise oligonucleotide which are useful as primers forperforming PCR methods. It is preferred that diagnostic kits accordingto the present invention comprise a container comprising a size markerto be run as a standard on a gel used to detect the presence ofamplified DNA. The size marker is the same size as the DNA generated bythe primers in the presence of the the CRCA-1 transcript or cDNAgenerated therefrom. Additional components in some kits includeinstructions for carrying out the assay. Additionally the kit mayoptionally comprise depictions or photographs that represent theappearence of positive and negative results.

PCR assays are useful for detecting the CRCA-1 transcript in homogenizedtissue samples and cells in body fluid samples. It is contemplated thatPCR on the plasma portion of a fluid sample could be used to detect theCRCA-1 transcript.

Another method of determining whether a sample contains cells expressingCRCA-1 is by branched chain oligonucleotide hybridization analysis ofmRNA extracted from a sample. Branched chain oligonucleotidehybridization may be performed as described in U.S. Pat. No. 5,597,909,U.S. Pat. No. 5,437,977 and U.S. Pat. No. 5,430,138, which are eachincorporated herein by reference. Reagents may be designed following theteachings of those patents and that sequence of the CCRA-1 transcript.

Another method of determining whether a sample contains cells expressingCRCA-1 is by Northern Blot analysis of mRNA extracted from anon-colorectal sample. The techniques for performing Northern blotanalyses are well known by those having ordinary skill in the art andare described in Sambrook, J. et al., (1989) Molecular Cloning: ALaboratory Manual, Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y. mRNA extraction, electrophoretic separation of the mRNA,blotting, probe preparation and hybridization are all well knowntechniques that can be routinely performed using readily availablestarting material.

The mRNA is extracted using poly dT columns and the material isseparated by electrophoresis and, for example, transferred tonitrocellulose paper. Labelled probes made from an isolated specificfragment or fragments can be used to visualize the presence of acomplementary fragment fixed to the paper. Probes useful to identifymRNA in a Northern Blot have a nucleotide sequence that is complementaryto the CRCA-1 transcript. Those having ordinary skill in the art coulduse the sequence information in SEQ ID NO:1 to design such probes or toisolate and clone the the CRCA-1 transcript or cDNA generated therefromto be used as a probe. Such probes are at least 15 nucleotides,preferably 30–200, more preferably 40–100 nucleotide fragments and maybe the entire CRCA-1 transcript.

According to the invention, diagnostic kits can be assembled which areuseful to practice methods of detecting the presence of the CRCA-1transcript in non-colorectal samples by Northern blot analysis. Suchdiagnostic kits comprise oligonucleotide which are useful as probes forhybridizing to the mRNA. The probes may be radiolabelled. It ispreferred that diagnostic kits according to the present inventioncomprise a container comprising a size marker to be run as a standard ona gel. It is preferred that diagnostic kits according to the presentinvention comprise a container comprising a positive control which willhybridize to the probe. Additional components in some kits includeinstructions for carrying out the assay. Additionally the kit mayoptionally comprise depictions or photographs that represent theappearence of positive and negative results.

Northern blot analysis is useful for detecting the CRCA-1 transcript inhomogenized tissue samples and cells in body fluid samples. It iscontemplated that PCR on the plasma portion of a fluid sample could beused to detect the CRCA-1 transcript.

Another method of detecting the presence of the CRCA-1 transcript byoligonucleotide hybridization technology. Oligonucleotide hybridizationtechnology is well known to those having ordinary skill in the art.Briefly, detectable probes which contain a specific nucleotide sequencethat will hybridize to nucleotide sequence of the CRCA-1 transcript. RNAor cDNA made from RNA from a sample is fixed, usually to filter paper orthe like. The probes are added and maintained under conditions thatpermit hybridization only if the probes fully complement the fixedgenetic material. The conditions are sufficiently stringent to wash offprobes in which only a portion of the probe hybridizes to the fixedmaterial. Detection of the probe on the washed filter indicatecomplementary sequences.

Probes useful in oligonucleotide assays at least 18 nucleotides ofcomplementary DNA and may be as large as a complete complementarysequence to the CRCA-1 transcript. In some preferred embodiments theprobes of the invention are 30–200 nucleotides, preferably 40–100nucleotides. The probes preferably contain a sequence that is uniquewith respect to the sequence that encodes the ST receptor.

One having ordinary skill in the art, using the sequence informationdisclosed in SEQ ID NO:1 can design probes which are fully complementaryto the CRCA-1 transcript but not the sequence that encodes ST receptor.Hybridization conditions can be routinely optimized to minimizebackground signal by non-fully complementary hybridization. In somepreferred embodiments, the probes are full length clones. Probes are atleast 15 nucleotides, preferably 30–200, more preferably 40–100nucleotide fragments and may be the entire CRCA-1 transcript.

The present invention includes labelled oligonucleotide which are usefulas probes for performing oligonucleotide hybridization. That is, theyare fully complementary with the CRCA-1 transcript but not the STreceptor transcript. For example, the mRNA sequence includes portionsencoded by different exons. The labelled probes of the present inventionare labelled with radiolabelled nucleotides or are otherwise detectableby readily available nonradioactive detection systems.

According to the invention, diagnostic kits can be assembled which areuseful to practice oligonucleotide hybridization methods of theinvention. Such diagnostic kits comprise a labelled oligonucleotidewhich encodes portions of the CRCA-1 transcript different from codingsequences that encode ST receptor. It is preferred that labelled probesof the oligonucleotide diagnostic kits according to the presentinvention are labelled with a radionucleotide. The oligonucleotidehybridization-based diagnostic kits according to the inventionpreferably comprise DNA samples that represent positive and negativecontrols. A positive control DNA sample is one that comprises a nucleicacid molecule which has a nucleotide sequence that is fullycomplementary to the probes of the kit such that the probes willhybridize to the molecule under assay conditions. A negative control DNAsample is one that comprises at least one nucleic acid molecule, thenucleotide sequence of which is partially complementary to the sequencesof the probe of the kit. Under assay conditions, the probe will nothybridize to the negative control DNA sample. Additional components insome kits include instructions for carrying out the assay. Additionallythe kit may optionally comprise depictions or photographs that representthe appearence of positive and negative results.

Oligonucleotide hybridization techniques are useful for detecting theCRCA-1 transcript in homogenized tissue samples and cells in body fluidsamples. It is contemplated that PCR on the plasma portion of a fluidsample could be used to detect the CRCA-1 transcript.

The present invention relates to in vitro kits for evaluating tissuessamples to determine the level of metastasis and to reagents andcompositions useful to practice the same.

In some embodiments of the invention, tissue samples that includeportions of the lamina propria may be isolated from individualsundergoing or recovery from surgery to remove colorectal tumors includeresection or colonoscopy. The tissue is analyzed to identify thepresence or absence of the CRCA-1 transcript. Techniques such asimmunohistochemistry assays may be performed to determine whether theone or more CRCA-1 translation products is present in cells in thetissue sample which are indicative of metastatic migration. In someembodiments of the invention, tissue samples are analyzed to identifywhether the CRCA-1 is being expressed in cells in the tissue samplewhich indicate metastatic migration by detecting the presence or absenceof the CRCA-1 transcript or one or more CRCA-1 translation products. Thepresence of the CRCA-1 transcript or cDNA generated therefrom can bedetermined using techniques such as in situ hybridization orimmunohistochemistry.

The present invention relates to in vitro kits for evaluating samples oftumors to determine whether or not they are colorectal in origin and toreagents and compositions useful to practice the same. In someembodiments of the invention, tumor samples may be isolated fromindividuals undergoing or recovery from surgery to remove tumors in thecolon, tumors in other organs or biopsy material. The tumor sample isanalyzed to identify the presence or absence of the CRCA-1 transcript.Techniques such as immunohistochemistry assays may be performed todetermine whether one or more CRCA-1 translation products are present incells in the tumor sample which are indicative of colorectal origin.Alternatively, in some embodiments of the invention, lumen tissuesamples are analyzed to identify whether CRCA-1 is being expressed incells in the tumor sample which indicate colorectal origin by detectingthe presence or absence of the CRCA-1 transcript or one or more CRCA-1translation products. The presence of mRNA that encodes the ST receptorprotein or cDNA generated therefrom can be determined using techniquessuch as in situ hybridization, immunohistochemistry and in situ STbinding assay.

In situ hybridization technology is well known by those having ordinaryskill in the art. Briefly, cells are fixed and detectable probes whichcontain a specific nucleotide sequence are added to the fixed cells. Ifthe cells contain complementary nucleotide sequences, the probes, whichcan be detected, will hybridize to them.

Probes useful in oligonucleotide assays at least 18 nucleotides ofcomplementary DNA and may be as large as a complete complementarysequence to the CRCA-1 transript. In some preferred embodiments theprobes of the invention are 30–200 nucleotides, preferably 40–100nucleotides. The probes contain a sequence that is unique from thosethat encode the ST receptor.

One having ordinary skill in the art, using the sequence information setforth in SEQ ID NO:1 and the known sequence for human ST receptor mRNAcan design probes useful in in situ hybridization technology to identifycells that express CRCA-1. Probes preferably hybridizes to a nucleotidesequence that corresponds to the CRCA-1 transcript. Hybridizationconditions can be routinely optimized to minimize background signal bynon-fully complementary hybridization and cross hybridization tosequences encoding ST receptors. Probes preferably hybridize to the fulllength CRCA-1 transcript. Probes are at least 15 nucleotides, preferably30–200, more preferably 40–100 nucleotide fragments and may be the CRCAtranscript, more preferably 18–28 nucleotide fragments of the CRCA-1transcript.

The probes are fully complementary and do not hybridize well topartially complementary sequences. For in situ hybridization accordingto the invention, it is preferred that the probes are detectable byfluorescence. A common procedure is to label probe with biotin-modifiednucleotide and then detect with fluorescently tagged avidin. Hence,probe does not itself have to be labelled with florescent but can besubsequently detected with florescent marker.

The present invention includes labelled oligonucleotide which are usefulas probes for performing oligonucleotide hybridization. That is, theyare fully complementary with mRNA sequences but not genomic sequences orST recpetor mRNA. For example, the mRNA sequence includes portionsencoded by different exons. The labelled probes of the present inventionare labelled with radiolabelled nucleotides or are otherwise detectableby readily available nonradioactive detection systems.

The present invention relates to probes useful for in situ hybridizationto identify cells that express CRCA-1.

Cells are fixed and the probes are added to the genetic material. Probeswill hybridize to the complementary nucleic acid sequences present inthe sample. Using a fluorescent microscope, the probes can be visualizedby their fluorescent markers.

According to the invention, diagnostic kits can be assembled which areuseful to practice in situ hybridization methods of the invention arefully complementary with mRNA sequences but not genomic sequences. Forexample, the mRNA sequence includes different exon sequences. It ispreferred that labelled probes of the in situ diagnostic kits accordingto the present invention are labelled with a fluorescent marker.

Those having ordinary skill in the art can analyze the fixed cells tocharacterize the level of metastatic migration of the colon cancercells. The labelling of colon-derived cells allows for improvedanalysis.

Immunohistochemistry techniques may be used to identify and essentiallystain cells with one or more CRCA-1 translation products. Such“staining” allows for analysis of metastatic migration. Anti-CRCA-1translation product antibodies such as those described above ofcontacted with fixed cells and the CRCA-1 translation products presentin the cells reacts with the antibodies. The antibodies are detectablylabelled or detected using labelled second antibody or protein A tostain the cells.

The techniques described herein for evaluating tumor sections can alsobe used to analyze tissue sections for samples of lymph nodes as well asother tissues to identify the presence of colorectal tumor cells. Thesamples can be prepared and “stained” to detect expression of CRCA-1.

In Vivo Imaging and Therapeutics

According to some embodiments of the invention, compositions and in vivomethods are provided for detecting, imaging, or treating colorectaltumors in an individual.

The conjugated compositions of the present invention are useful fortargeting cells that line the inner intestine wall including cancercells derived from such cells, particularly metastasized cancer cellsderived from such cells.

When the conjugated compositions of the present invention areadministered outside the intestinal tract such as when administered inthe circulatory system, they remain segregated from the cells that linethe intestinal tract and will bind only to cells outside the intestinaltract which are derived from the intestinal tract such as metastasizedcolorectal cells. The conjugated compositions will not bind tonon-colorectal derived cells. Thus, the active moieties of conjugatedcompositions administered outside the intestinal tract are delivered tocells which are derived from the intestinal tract such as metastasizedcolorectal cells but will not be delivered to any other cells.

Therapeutic and diagnostic pharmaceutical compositions of the presentinvention include conjugated compounds specifically targeted tometastatic disease. These conjugated compounds include moieties thatbind to one or more CRCA-1 translation products which do not bind tocells of normal tissue in the body except cells of the intestinal tractsince the cells of other tissues do not possess such translationproducts. Further, according to the invention, the CRCA-1 translationproduct binding moieties do not bind to ST receptors.

Unlike normal colorectal cells and localized colorectal cancer cells,metastasized colorectal cancer cells are accessible to substancesadministered outside the intestinal tract, for example administered inthe circulatory system. The only CRCA-1 translation products in normaltissue exist in the apical membranes of intestinal mucosa cells and thuseffectively isolated from the targeted cancer chemotherapeutics andimaging agents administered outside the intestinal tract by theintestinal mucosa barrier. Thus, metastasized colorectal cells may betargeted by conjugated compounds of the present invention by introducingsuch compounds outside the intestinal tract such as for example byadministering pharmaceutical compositions that comprise conjugatedcompounds into the circulatory system.

One having ordinary skill in the art can identify individuals suspectedof suffering from colorectal cancer and metastasized colorectal cells.In those individuals diagnosed with colorectal cancer, it is standardtherapy to suspect metastasis and aggressively attempt to eradicatemetastasized cells. The present invention provides pharmaceuticalcompositions and methods for imaging and thereby will more definitivelydiagnose metastasis. Further, the present invention providespharmaceutical compositions comprising therapeutic agents and methodsfor specifically targeting and eliminating metastasized colorectalcancer cells. Further, the present invention provides pharmaceuticalcompositions that comprise therapeutics and methods for specificallyeliminating colorectal cancer cells.

The pharmaceutical compositions which comprise conjugated compositionsof the present invention may be used to diagnose or treat individualssuffering from localized colorectal tumors, that is primary ornon-metastatic colorectal tumors if these have penetrated the basementmembrane underlying the mucosa into the submucosa where there isabundant blood supply to which they have access. Penetration into thesubmucosa circumvents the mucosal barrier resulting in the ability ofconjugated compositions introduced into the circulatory system tointeract with these tumors.

The present invention relies upon the use of a CRCA-1 translationproduct binding moiety in a conjugated composition. The CRCA-1translation product binding moiety is essentially a portion of theconjugated composition which acts as a ligand to a CRCA-1 translationproduct and thus specifically binds to it. The conjugated compositionalso includes an active moiety which is associated with the CRCA-1translation product binding moiety; the active moiety being an activeagent which is either useful to image, target, neutralize or kill thecell.

According to the present invention, the CRCA-1 translation productbinding moiety is the CRCA-1 translation product ligand portion of aconjugated composition. In some embodiments, the CRCA-1 translationproduct ligand is an antibody.

In some preferred embodiments, conjugated compounds comprise CRCA-1translation product binding moieties that comprise an anti-CRCA-1translation product antibody.

It is preferred that the CRCA-1 translation product ligand used as theCRCA-1 translation product binding moiety be as small as possible. Thusit is preferred that the CRCA-1 translation product ligand be anon-peptide small molecule or small peptide, preferably less than 25amino acids, more preferably less than 20 amino acids. In someembodiments, the CRCA-1 translation product ligand which constitute theCRCA-1 translation product binding moiety of a conjugated composition isless than 15 amino acids. CRCA-1 translation product binding peptidecomprising less than 10 amino acids and CRCA-1 translation productbinding peptide less than 5 amino acids may be used as CRCA-1translation product binding moieties according to the present invention.It is within the scope of the present invention to include largermolecules which serve as CRCA-1 translation product binding moietiesincluding, but not limited to molecules such as antibodies whichspecifically bind to CRCA-1 translation product.

CRCA-1 translation product ligands useful as CRCA-1 translation productbinding moieties may be identifed using various well known combinatoriallibrary screening technologies such as those set forth in Example 1herein.

An assay may be used to test both peptide and non-peptide compositionsto determine whether or not they are CRCA-1 translation product ligandsor, to test conjugated compositions to determine if they possess CRCA-1translation product binding activity. Such compositions thatspecifically bind to CRCA-1 translation product can be identified by acompetitive binding assay using antibodies known to bind to the CRCA-1translation product. The competitive binding assay is a standardtechnique in pharmacology which can be readily performed by those havingordinary skill in the art using readily available starting materials.

CRCA-1 translation products may be produced synthetically, recombinantlyor isolated from natural sources.

Using a solid phase synthesis as an example, the protected orderivatized amino acid is attached to an inert solid support through itsunprotected carboxyl or amino group. The protecting group of the aminoor carboxyl group is then selectively removed and the next amino acid inthe sequence having the complementary (amino or carboxyl) group suitablyprotected is admixed and reacted with the residue already attached tothe solid support. The protecting group of the amino or carboxyl groupis then removed from this newly added amino acid residue, and the nextamino acid (suitably protected) is then added, and so forth. After allthe desired amino acids have been linked in the proper sequence, anyremaining terminal and side group protecting groups (and solid support)are removed sequentially or concurrently, to provide the final peptide.The peptide of the invention are preferably devoid of benzylated ormethylbenzylated amino acids. Such protecting group moieties may be usedin the course of synthesis, but they are removed before the peptides areused. Additional reactions may be necessary, as described elsewhere, toform intramolecular linkages to restrain conformation.

CRCA-1 translation products and conjugated compositions or portionsthereof which are peptides may also be prepared by recombinant DNAtechniques. Provision of a suitable DNA sequence encoding the desiredpeptide permits the production of the peptide using recombinanttechniques now known in the art. The coding sequence can be obtainedfrom natural sources or synthesized or otherwise constructed usingwidely available starting materials by routine methods. When the codingDNA is prepared synthetically, advantage can be taken of known codonpreferences of the intended host where the DNA is to be expressed.

To produce a CRCA-1 translation product which occurs in nature, onehaving ordinary skill in the art can, using well-known techniques,obtain a DNA molecule encoding the CRCA-1 translation product and insertthat DNA molecule into a commercially available expression vector foruse in well-known expression systems such as for example those describedherein.

For example, the commercially available plasmid pSE420 (Invitrogen, SanDiego, Calif.) may be used for recombinant production in E. coli. Thecommercially available plasmid pYES2 (Invitrogen, San Diego, Calif.) maybe used for production in S. cerevisiae strains of yeast. Thecommercially available MaxBac™ (Invitrogen, San Diego, Calif.) completebaculovirus expression system may be used for production in insectcells. The commercially available plasmid pcDNA I (Invitrogen, SanDiego, Calif.) may be used for production in mammalian cells such asChinese Hamster Ovary cells.

One having ordinary skill in the art may use these or other commerciallyavailable expression vectors and systems or produce vectors usingwell-known methods and readily available starting materials. Expressionsystems containing the requisite control sequences, such as promotersand polyadenylation signals, and preferably enhancers, are readilyavailable and known in the art for a variety of hosts. See e.g.,Sambrook et al., Molecular Cloning a Laboratory Manual, Second Ed. ColdSpring Harbor Press (1989). Thus, the desired proteins can be preparedin both prokaryotic and eukaryotic systems, resulting in a spectrum ofprocessed forms of the protein.

The most commonly used prokaryotic system remains E. coli, althoughother systems such as B. subtilis and Pseudomonas are also useful.Suitable control sequences for prokaryotic systems include bothconstitutive and inducible promoters including the lac promoter, the trppromoter, hybrid promoters such as tac promoter, the lambda phage P1promoter. In general, foreign proteins may be produced in these hostseither as fusion or mature proteins. When the desired sequences areproduced as mature proteins, the sequence produced may be preceded by amethionine which is not necessarily efficiently removed. Accordingly,the peptides and proteins claimed herein may be preceded by anN-terminal Met when produced in bacteria. Moreover, constructs may bemade wherein the coding sequence for the peptide is preceded by anoperable signal peptide which results in the secretion of the protein.When produced in prokaryotic hosts in this matter, the signal sequenceis removed upon secretion.

A wide variety of eukaryotic hosts are also now available for productionof recombinant foreign proteins. As in bacteria, eukaryotic hosts may betransformed with expression systems which produce the desired proteindirectly, but more commonly signal sequences are provided to effect thesecretion of the protein. Eukaryotic systems have the additionaladvantage that they are able to process introns which may occur in thegenomic sequences encoding proteins of higher organisms. Eukaryoticsystems also provide a variety of processing mechanisms which result in,for example, glycosylation, carboxy-terminal amidation, oxidation orderivatization of certain amino acid residues, conformational control,and so forth.

Commonly used eukaryotic systems include, but are not limited to, yeast,fungal cells, insect cells, mammalian cells, avian cells, and cells ofhigher plants. Suitable promoters are available which are compatible andoperable for use in each of these host types as well as are terminationsequences and enhancers, as e.g. the baculovirus polyhedron promoter. Asabove, promoters can be either-constitutive or inducible. For example,in mammalian systems, the mouse metallothionene promoter can be inducedby the addition of heavy metal ions.

The particulars for the construction of expression systems suitable fordesired hosts are known to those in the art. For recombinant productionof the protein, the DNA encoding it is suitably ligated into theexpression vector of choice and then used to transform the compatiblehost which is then cultured and maintained under conditions whereinexpression of the foreign gene takes place. The protein of the presentinvention thus produced is recovered from the culture, either by lysingthe cells or from the culture medium as appropriate and known to thosein the art.

One having ordinary skill in the art can, using well-known techniques,isolate the protein that is produced.

According to the present invention, the active moiety may be atherapeutic agent or an imaging agent. One having ordinary skill in theart can readily recognize the advantages of being able to specificallytarget metastasized colorectal cells with an CRCA-1 translation productligand and conjugate such a ligand with many different active agents.

Chemotherapuetics useful as active moieties which when conjugated to aCRCA-1 translation product binding moiety are specifically delivered tometastasized colorectal cells are typically, small chemical entitiesproduced by chemical synthesis. Chemotherapeutics include cytotoxic andcytostatic drugs. Chemotherapeutics may include those which have othereffects on cells such as reversal of the transformed state to adifferentiated state or those which inhibit cell replication. Examplesof chemotherapeutics include common cytotoxic or cytostatic drugs suchas for example: methotrexate (amethopterin), doxorubicin (Adriamycin™),daunorubicin, cytosinarabinoside, etoposide, 5-4 fluorouracil,melphalan, chlorambucil, and other nitrogen mustards (e.g.cyclophosphamide), cis-platinum, vindesine (and other vinca alkaloids),mitomycin and bleomycin. Other chemotherapeutics include: purothionin(barley flour oligopeptide), macromomycin, 1,4-benzoquinone derivativesand trenimon.

Toxins are useful as active moieties. When a toxin is conjugated to aCRCA-1 translation product binding moiety, the conjugated composition isspecifically delivered to a metastasized colorectal cell by way of theCRCA-1 translation product binding moiety and the toxin moiety kills thecell. Toxins are generally complex toxic products of various organismsincluding bacteria, plants, etc. Examples of toxins include but are notlimited to: ricin, ricin A chain (ricin toxin), Pseudomonas exotoxin(PE), diphtheria toxin (DT), Clostridium perfringens phospholipase C(PLC), bovine pancreatic ribonuclease (BPR), pokeweed antiviral protein(PAP), abrin, abrin A chain (abrin toxin), cobra venom factor (CVF),gelonin (GEL), saporin (SAP), modeccin, viscumin and volkensin. Asdiscussed above, when protein toxins are employed with CRCA-1translation product binding peptides, conjugated compositions may beproduced using recombinant DNA techniques. Briefly, a recombinant DNAmolecule can be constructed which encodes both the CRCA-1 translationproduct ligand and the toxin on a chimeric gene. When the chimeric geneis expressed, a fusion protein is produced which includes a CRCA-1translation product binding moiety and an active moiety. Protein toxinsare also useful to form conjugated compounds with CRCA-1 translationproduct binding peptides through non-peptidyl bonds.

In addition, there are other approaches for utilizing active agents forthe treatment of cancer. For example, conjugated compositions may beproduced which include a CRCA-1 translation product binding moiety andan active moiety which is an active enzyme. The CRCA-1 translationproduct binding moiety specifically localizes the conjugated compositionto the tumor cells. An inactive prodrug which can be converted by theenzyme into an active drug is administered to the patient. The prodrugis only converted to an active drug by the enzyme which is localized tothe tumor. An example of an enzyme/prodrug pair includes alkalinephosphatase/etoposidephosphate. In such a case, the alkaline phosphataseis conjugated to a CRCA-1 translation product binding ligand. Theconjugated compound is administered and localizes at the metastasizedcell. Upon contact with etoposidephosphate (the prodrug), theetoposidephosphate is converted to etoposide, a chemotherapeutic drugwhich is taken up by the cancer cell.

Radiosensitizing agents are substances that increase the sensitivity ofcells to radiation. Examples of radiosensitizing agents includenitroimidazoles, metronidazole and misonidazole (see: DeVita, V. T. Jr.in Harrison's Principles of Internal Medicine, p. 68, McGraw-Hill BookCo., N.Y. 1983, which is incorporated herein by reference). Theconjugated compound that comprises a radiosensitizing agent as theactive moiety is administered and localizes at the metastasized cell.Upon exposure of the individual to radiation, the radiosensitizing agentis “excited” and causes the death of the cell.

Radionuclides may be used in pharmaceutical compositions that are usefulfor radiotherapy or imaging procedures.

Examples of radionuclides useful as toxins in radiation therapy include:⁴⁷Sc, ⁶⁷Cu, ⁹⁰Y, ¹⁰⁹Pd, ¹²³I, ¹²⁵I, ¹³¹I, ¹⁸⁶Re, ¹⁸⁸Re, ¹⁹⁹Au, ²¹¹At,²¹²Pb and ²¹²B. Other radionuclides which have been used by those havingordinary skill in the art include: ³²P and ³³P, ⁷¹Ge, ⁷⁷As, ¹⁰³Pb,¹⁰⁵Rh, ¹³¹Ag, ¹¹⁰Sb, ¹²¹Sn, ¹³¹Cs, ¹⁴³Pr, ¹⁶¹Tb, ¹⁷⁷Lu, ¹⁹¹Os,^(193M)Pt, ¹⁹⁷Hg, all beta negative and/or auger emitters. Somepreferred radionuclides include: ⁹⁰Y, ¹³¹I ²¹¹At and ²¹²Pb/²¹²Bi.

According to the present invention, the active moieties may be animaging agent. Imaging agents are useful diagnostic procedures as wellas the procedures used to identify the location of metastasized cells.Imaging can be performed by many procedures well-known to those havingordinary skill in the art and the appropriate imaging agent useful insuch procedures may be conjugated to a CRCA-1 translation product ligandby well-known means. Imaging can be performed, for example, byradioscintigraphy, nuclear magnetic resonance imaging (MRI) or computedtomography (CT scan). The most commonly employed radionuclide imagingagents include radioactive iodine and indium. Imaging by CT scan mayemploy a heavy metal such as iron chelates. MRI scanning may employchelates of gadolinium or manganese. Additionally, positron emissiontomography (PET) may be possible using positron emitters of oxygen,nitrogen, iron, carbon, or gallium. Example of radionuclides useful inimaging procedures include: ⁴³K, ⁵²Fe, ⁵⁷Co, ⁶⁷Cu, ⁶⁷Ga, ⁶⁸Ga, ⁷⁷Br,⁸¹Rb/^(81M)Kr, ^(87M)Sr, ^(99M)Tc, ¹¹¹In, ^(113M)In, ¹²³I, ¹²⁵I, ¹²⁷Cs,¹²⁹Cs, ¹³¹I, ¹³²I, ¹⁹⁷Hg, ²⁰³Pb and ²⁰⁶Bi.

It is preferred that the conjugated compositions be non-immunogenic orimmunogenic at a very low level. Accordingly, it is preferred that theCRCA-1 translation product binding moiety be a small, poorly immunogenicor non-immunogenic peptide or a non-peptide. Alternatively, the CRCA-1translation product binding moiety may be a humanized or primatizedantibody or a human antibody.

CRCA-1 translation product ligands are conjugated to active agents by avariety of well-known techniques readily performed without undueexperimentation by those having ordinary skill in the art. The techniqueused to conjugate the CRCA-1 translation product ligand to the activeagent is dependent upon the molecular nature of the CRCA-1 translationproduct ligand and the active agent. After the CRCA-1 translationproduct ligand and the active agent are conjugated to form a singlemolecule, assays may be performed to ensure that the conjugated moleculeretains the activities of the moieties. The competitive binding assaydescribed above may be used to confirm that the CRCA-1 translationproduct binding moiety retains its binding activity as a conjugatedcompound. Similarly, the activity of the active moiety may be testedusing various assays for each respective type of active agent.Radionuclides retain there activity, i.e. their radioactivity,irrespective of conjugation. With respect to active agents which aretoxins, drugs and targeting agents, standard assays to demonstrate theactivity of unconjugated forms of these compounds may be used to confirmthat the activity has been retained.

Conjugation may be accomplished directly between the CRCA-1 translationproduct ligand and the active agent or linking, intermediate moleculargroups may be provided between the CRCA-1 translation product ligand andthe active agent. Crosslinkers are particularly useful to facilitateconjugation by providing attachment sites for each moiety. Crosslinkersmay include additional molecular groups which serve as spacers toseparate the moieties from each other to prevent either from interferingwith the activity of the other.

One having ordinary skill in the art may conjugate a CRCA-1 translationproduct ligand to a chemotherapeutic drug using well-known techniques.For example, Magerstadt, M. Antibody Conjugates and Malignant Disease.(1991) CRC Press, Boca Raton, USA, pp. 110–152) which is incorporatedherein by reference, teaches the conjugation of various cytostatic drugsto amino acids of antibodies. Such reactions may be applied to conjugatechemotherapeutic drugs to CRCA-1 translation product ligands, includinganti-CRCA-1 translation product antibodies, with an appropriate linker.Most of the chemotherapeutic agents currently in use in treating cancerpossess functional groups that are amenable to chemical crosslinkingdirectly with proteins. For example, free amino groups are available onmethotrexate, doxorubicin, daunorubicin, cytosinarabinoside, cis-platin,vindesine, mitomycin and bleomycin while free carboxylic acid groups areavailable on methotrexate, melphalan, and chlorambucil. These functionalgroups, that is free amino and carboxylic acids, are targets for avariety of homobifunctional and heterobifunctional chemical crosslinkingagents which can crosslink these drugs directly to the single free aminogroup of an antibody. For example, one procedure for crosslinking CRCA-1translation product ligands which have a free amino group to activeagents which have a free amino group such as methotrexate, doxorubicin,daunorubicin, cytosinarabinoside, cis-platin, vindesine, mitomycin andbleomycin, or alkaline phosphatase, or protein- or peptide-based toxinemploys homobifunctional succinimidyl esters, preferably with carbonchain spacers such as disuccinimidyl suberate (Pierce Co, Rockford,Ill.). In the event that a cleavable conjugated compound is required,the same protocol would be employed utilizing 3,3′-dithiobis(sulfosuccinimidylpropionate; Pierce Co.).

In order to conjugate a CRCA-1 translation product ligand that is apeptiode or protein to a peptide-based active agent such as a toxin, theCRCA-1 translation product ligand and the toxin may be produced as asingle, fusion protein either by standard peptide synthesis orrecombinant DNA technology, both of which can be routinely performed bythose having ordinary skill in the art. Alternatively, two peptides, theCRCA-1 translation product ligand peptide and the peptide-based toxinmay be produced and/or isolated as separate peptides and conjugatedusing crosslinkers. As with conjugated compositions that containchemotherapeutic drugs, conjugation of CRCA-1 translation productbinding peptides and toxins can exploit the ability to modify the singlefree amino group of a CRCA-1 translation product binding peptide whilepreserving the receptor-binding function of this molecule.

One having ordinary skill in the art may conjugate a CRCA-1 translationproduct ligand to a radionuclide using well-known techniques. Forexample, Magerstadt, M. (1991) Antibody Conjugates And MalignantDisease, CRC Press, Boca Raton, FLA; and Barchel, S. W. and Rhodes, B.H., (1983) Radioimaging and Radiotherapy, Elsevier, NY, N.Y., each ofwhich is incorporated herein by reference, teach the conjugation ofvarious therapeutic and diagnostic radionuclides to amino acids ofantibodies.

The present invention provides pharmaceutical compositions that comprisethe conjugated compounds of the invention and pharmaceuticallyacceptable carriers or diluents. The pharmaceutical composition of thepresent invention may be formulated by one having ordinary skill in theart. Suitable pharmaceutical carriers are described in Remington'sPharmaceutical Sciences, A. Osol, a standard reference text in thisfield, which is incorporated herein by reference. In carrying outmethods of the present invention, conjugated compounds of the presentinvention can be used alone or in combination with other diagnostic,therapeutic or additional agents. Such additional agents includeexcipients such as coloring, stabilizing agents, osmotic agents andantibacterial agents. Pharmaceutical compositions are preferably sterileand pyrogen free.

The conjugated compositions of the invention can be, for example,formulated as a solution, suspension or emulsion in association with apharmaceutically acceptable parenteral vehicle. Examples of suchvehicles are water, saline, Ringer's solution, dextrose solution, and 5%human serum albumin. Liposomes may also be used. The vehicle may containadditives that maintain isotonicity (e.g., sodium chloride, mannitol)and chemical stability (e.g., buffers and preservatives). Theformulation is sterilized by commonly used techniques. For example, aparenteral composition suitable for administration by injection isprepared by dissolving 1.5% by weight of active ingredient in 0.9%sodium chloride solution.

The pharmaceutical compositions according to the present invention maybe administered as either a single dose or in multiple doses. Thepharmaceutical compositions of the present invention may be administeredeither as individual therapeutic agents or in combination with othertherapeutic agents. The treatments of the present invention may becombined with conventional therapies, which may be administeredsequentially or simultaneously.

The pharmaceutical compositions of the present invention may beadministered by any means that enables the conjugated composition toreach the targeted cells. In some embodiments, routes of administrationinclude those selected from the group consisting of intravenous,intraarterial, intraperitoneal, local administration into the bloodsupply of the organ in which the tumor resides or directly into thetumor itself. Intravenous administration is the preferred mode ofadministration. It may be accomplished with the aid of an infusion pump.

The dosage administered varies depending upon factors such as: thenature of the active moiety; the nature of the conjugated composition;pharmacodynamic characteristics; its mode and route of administration;age, health, and weight of the recipient; nature and extent of symptoms;kind of concurrent treatment; and frequency of treatment.

Because conjugated compounds are specifically targeted to cells with oneor more CRCA-1 translation products, conjugated compounds which comprisechemotherapeutics or toxins are administered in doses less than thosewhich are used when the chemotherapeutics or toxins are administered asunconjugated active agents, preferably in doses that contain up to 100times less active agent. In some embodiments, conjugated compounds whichcomprise chemotherapeutics or toxins are administered in doses thatcontain 10–100 times less active agent as an active moiety than thedosage of chemotherapeutics or toxins administered as unconjugatedactive agents. To determine the appropriate dose, the amount of compoundis preferably measured in moles instead of by weight. In that way, thevariable weight of different CRCA-1 translation product binding moietiesdoes not affect the calculation. Presuming a one to one ratio of CRCA-1translation product binding moiety to active moiety in conjugatedcompositions of the invention, less moles of conjugated compounds may beadministered as compared to the moles of unconjugated compoundsadministered, preferably up to 100 times less moles.

Typically, chemotherapeutic conjugates are administered intravenously inmultiple divided doses.

Up to 20 gm IV/dose of methotrexate is typically administered in anunconjugated form. When methotrexate is administered as the activemoiety in a conjugated compound of the invention, there is a 10- to100-fold dose reduction. Thus, presuming each conjugated compoundincludes one molecule of methotrexate conjugated to one CRCA-1translation product binding moiety, of the total amount of conjugatedcompound administered, up to about 0.2–2.0 g of methotrexate is presentand therefore administered. In some embodiments, of the total amount ofconjugated compound administered, up to about 200 mg–2 g of methotrexateis present and therefore administered.

To dose conjugated compositions comprising CRCA-1 translation productbinding moieties linked to active moieties that are radioisotopes inpharmaceutical compositions useful as imaging agents, it is presumedthat each CRCA-1 translation product binding moiety is linked to oneradioactive active moiety. The amount of radioisotope to be administeredis dependent upon the radioisotope. Those having ordinary skill in theart can readily formulate the amount of conjugated compound to beadministered based upon the specific activity and energy of a givenradionuclide used as an active moiety. Typically 0.1–100 millicuries perdose of imaging agent, preferably 1–10 millicuries, most often 2–5millicuries are administered. Thus, pharmaceutical compositionsaccording to the present invention useful as imaging agents whichcomprise conjugated compositions comprising a CRCA-1 translation productbinding moiety and a radioactive moiety comprise 0.1–100 millicuries, insome embodiments preferably 1–10 millicuries, in some embodimentspreferably 2–5 millicuries, in some embodiments more preferably 1–5millicuries. Examples of dosages include: ¹³¹I=between about 0.1–100millicuries per dose, in some embodiments preferably 1–10 millicuries,in some embodiments 2–5 millicuries, and in some embodiments about 4millicuries; ¹¹¹In=between about 0.1–100 millicuries per dose, in someembodiments preferably 1–10 millicuries, in some embodiments 1–5millicuries, and in some embodiments about 2 millicuries;^(99m)In=between about 0.1–100 millicuries per dose, in some embodimentspreferably 5–75 millicuries, in some embodiments 10–50 millicuries, andin some embodiments about 27 millicuries. Wessels B. W. and R. D. Rogus(1984) Med. Phys. 11:638 and Kwok, C. S. et al. (1985) Med. Phys.12:405, both of which are incorporated herein by reference, disclosedetailed dose calculations for diagnostic and therapeutic conjugateswhich may be used in the preparation of pharmaceutical compositions ofthe present invention which include radioactive conjugated compounds.

One aspect of the present invention relates to a method of treatingindividuals suspected of suffering from metastasized colorectal cancer.Such individuals may be treated by administering to the individual apharmaceutical composition that comprises a pharmaceutically acceptablecarrier or diluent and a conjugated compound that comprises a CRCA-1translation product binding moiety and an active moiety wherein theactive moiety is a radiostable therapeutic agent. In some embodiments ofthe present invention, the pharmaceutical composition comprises apharmaceutically acceptable carrier or diluent and a conjugated compoundthat comprises a CRCA-1 translation product binding moiety and an activemoiety wherein the active moiety is a radiostable active agent and theCRCA-1 translation product binding moiety is an antibody. In someembodiments of the present invention, the pharmaceutical compositioncomprises a pharmaceutically acceptable carrier or diluent and aconjugated compound that comprises a CRCA-1 translation product bindingmoiety and an active moiety wherein the active moiety is a radiostabletherapeutic agent. In some embodiments of the present invention, thepharmaceutical composition comprises a pharmaceutically acceptablecarrier or diluent and a conjugated compound that comprises a CRCA-1translation product binding moiety and an active moiety wherein theactive moiety is a radiostable active agent selected from the groupconsisting of: methotrexate, doxorubicin, daunorubicin,cytosinarabinoside, etoposide, 5-4 fluorouracil, melphalan,chlorambucil, cis-platinum, vindesine, mitomycin, bleomycin,purothionin, macromomycin, 1,4-benzoquinone derivatives, trenimon,ricin, ricin A chain, Pseudomonas exotoxin, diphtheria toxin,Clostridium perfringens phospholipase C, bovine pancreatic ribonuclease,pokeweed antiviral protein, abrin, abrin A chain, cobra venom factor,gelonin, saporin, modeccin, viscumin, volkensin, alkaline phosphatase,nitroimidazole, metronidazole and misonidazole. The individual beingtreated may be diagnosed as having metastasized colorectal cancer or maybe diagnosed as having localized colorectal cancer and may undergo thetreatment proactively in the event that there is some metastasis as yetundetected. The pharmaceutical composition contains a therapeuticallyeffective amount of the conjugated composition. A therapeuticallyeffective amount is an amount which is effective to cause a cytotoxic orcytostatic effect on metastasized colorectal cancer cells withoutcausing lethal side effects on the individual.

One aspect of the present invention relates to a method of treatingindividuals suspected of suffering from metastasized colorectal cancer.Such individuals may be treated by administering to the individual apharmaceutical composition that comprises a pharmaceutically acceptablecarrier or diluent and a conjugated compound that comprises a CRCA-1translation product binding moiety and an active moiety wherein theactive moiety is a radioactive. In some embodiments of the presentinvention, the pharmaceutical composition comprises a pharmaceuticallyacceptable carrier or diluent and a conjugated compound that comprises aCRCA-1 translation product binding moiety and an active moiety whereinthe active moiety is a radioactive and the ST receptor binding moiety isan antibody. In some embodiments of the present invention, thepharmaceutical composition comprises a pharmaceutically acceptablecarrier or diluent and a conjugated compound that comprises a CRCA-1translation product and an active moiety wherein the active moiety is aradioactive agent selected from the group consisting of: ⁴⁷Sc, ⁶⁷Cu,⁹⁰Y, ¹⁰⁹Pd, ¹²³I, ¹²⁵I, ¹³¹I, ¹⁸⁶Re, ¹⁸⁸Re, ¹⁹⁹Au, ²¹¹At, ²¹²Pb, ²¹²B,³²P and ³³P, ⁷¹Ge, ⁷⁷As, ¹⁰³Pb, ¹⁰⁵Rh, ¹¹¹Ag, ¹¹⁹Sb, ¹²¹ Sn, ¹³¹Cs,¹⁴³Pr, ¹⁶¹Tb, ¹⁷⁷Lu, ¹⁹¹Os, ^(193M)Pt, ¹⁹⁷Hg, ³²P and ³³P, ⁷¹Ge, ⁷⁷As,¹⁰³ Pb, ¹⁰⁵Rh, ¹¹¹Ag, ¹¹⁹Sb, ¹²¹Sn ¹³¹Cs, ¹⁴³Pr, ¹⁶¹Tb, ¹⁷⁷Lu, ¹⁹¹OS,^(193M)Pt, ¹⁹⁷Hg, all beta negative and/or auger emitters. Theindividual being treated may be diagnosed as having metastasizedcolorectal cancer or may be diagnosed as having localized colorectalcancer and may undergo the treatment proactively in the event that thereis some metastasis as yet undetected. The pharmaceutical compositioncontains a therapeutically effective amount of the conjugatedcomposition. A therapeutically effective amount is an amount which iseffective to cause a cytotoxic or cytostatic effect on metastasizedcolorectal cancer cells without causing lethal side effects on theindividual.

One aspect of the present invention relates to a method of detectingmetastasized colorectal cancer cells in an individual suspected ofsuffering from metastasized colorectal cancer by radioimaging. Suchindividuals may be diagnosed as suffering from metastasized colorectalcancer and the metastasized colorectal cancer cells may be detected byadministering to the individual, preferably by intravenousadministration, a pharmaceutical composition that comprises apharmaceutically acceptable carrier or diluent and a conjugated compoundthat comprises a CRCA-1 translation product binding moiety and an activemoiety wherein the active moiety is a radioactive and detecting thepresence of a localized accumulation or aggregation of radioactivity,indicating the presence of cells with a CRCA-1 translation product. Insome embodiments of the present invention, the pharmaceuticalcomposition comprises a pharmaceutically acceptable carrier or diluentand a conjugated compound that comprises a CRCA-1 translation productbinding moiety and an active moiety wherein the active moiety is aradioactive and the ST receptor binding moiety is an antibody. In someembodiments of the present invention, the pharmaceutical compositioncomprises a pharmaceutically acceptable carrier or diluent and aconjugated compound that comprises an ST receptor binding moiety and anactive moiety wherein the active moiety is a radioactive agent selectedfrom the group consisting of: radioactive heavy metals such as ironchelates, radioactive chelates of gadolinium or manganese, positronemitters of oxygen, nitrogen, iron, carbon, or gallium, ⁴³K, ⁵²Fe, ⁵⁷Co,⁶⁷Cu, ⁶⁷Ga, ⁶⁸Ga, ⁷⁷Br, ⁸¹Rb/^(81M)Kr, ^(87M)Sr, ^(99M)Tc, ¹¹¹In,^(113M)In, ¹²³I, ¹²⁵I, ¹²⁷Cs, ¹²⁹CS, ¹³¹I, ¹³²I, ¹⁹⁷Hg, ²⁰³Pb and ²⁰⁶Bi.The individual being treated may be diagnosed as having metastasizedcolorectal cancer or may be diagnosed as having localized colorectalcancer and may undergo the treatment proactively in the event that thereis some metastasis as yet undetected. The pharmaceutical compositioncontains a diagnostically effective amount of the conjugatedcomposition. A diagnostically effective amount is an amount which can bedetected at a site in the body where cells with ST receptors are locatedwithout causing lethal side effects on the individual.

Another aspect of the invention relates to unconjugated compositionswhich comprise a CRCA-1 translation product binding ligand and an activeagent. For example, liposomes are small vesicles composed of lipids.Drugs can be introduced into the center of these vesicles. The outershell of these vesicles comprise a CRCA-1 translation product bindingligand. Liposomes Volumes 1, 2 and 3 CRC Press Inc. Boca Raton FLA,which is incorporated herein by reference, disclose preparation ofliposome-encapsulated active agents which include targeting agents thatcorrespond to CRCA-1 translation product ligand in the outer shell.Unconjugated compositions which comprise a CRCA-1 translation productligand in the matrix of a liposome with an active agent inside includesuch compositions in which the CRCA-1 translation product ligand is sanantibody and the active agent is selected from the group consisting of:methotrexate, doxorubicin, daunorubicin, cytosinarabinoside, etoposide,5-4 fluorouracil, melphalan, chlorambucil, cis-platinum, vindesine,mitomycin, bleomycin, purothionin, macromomycin, 1,4-benzoquinonederivatives, trenimon, ricin, ricin A chain, Pseudomonas exotoxin,diphtheria toxin, Clostridium perfringens phospholipase C, bovinepancreatic ribonuclease, pokeweed antiviral protein, abrin, abrin Achain, cobra venom factor, gelonin, saporin, modeccin, viscumin,volkensin, alkaline phosphatase, nitroimidazole, metronidazole andmisonidazole.

Drug Delivery Targeted to Colon Cells Generally

Another aspect of the invention relates to unconjugated and conjugatedcompositions which comprise a CRCA-1 translation product ligand used todeliver therapeutic nucleic acid molecules to cells that comprise aCRCA-1 translation product such as normal and cancer cells of theintestinal tract as well as metastasized colorectal cancer cells. Insome embodiments, the genetic material is delivered to metastasizedtumor cells to produce an antigen that can be targeted by the immunesystem or to produce a protein which kills the cell or inhibits itsproliferation. In some embodiments, the CRCA-1 translation productligand is used to deliver nucleic acids that encode nucleic acidmolecules which replace defective endogenous genes or which encodetherapeutic proteins. In some embodiments, the CRCA-1 translationproduct ligand is thus used to deliver the active agent specifically tothe cells lining the intestinal tract to treat diseases specific to thisorgan. According to this aspect of the invention, compositions comprisenucleic acid molecules which can replace defective genes. In someembodiments, the compositions are used in gene therapy protocols todeliver to individuals, genetic material needed and/or desired to makeup for a genetic deficiency.

In some embodiments, the CRCA-1 translation product ligand is combinedwith or incorporated into a delivery vehicle thereby converting thedelivery vehicle into a specifically targeted delivery vehicle. Forexample, a CRCA-1 translation product binding peptide may be integratedinto the outer portion of a viral particle making such a virus a CRCA-1translation product-bearing cell specific virus. Similarly, the coatprotein of a virus may be engineered such that it is produced as afusion protein which includes an active CRCA-1 translation productbinding peptide that is exposed or otherwise accessible on the outsideof the viral particle making such a virus a CRCA-1 translationproduct-bearing cell-specific virus. In some embodiments, a CRCA-1translation product ligand may be integrated or otherwise incorporatedinto the liposomes wherein the CRCA-1 translation product ligand isexposed or otherwise accessible on the outside of the liposome makingsuch liposomes specifically targeted to CRCA-1 translationproduct-bearing cells.

The active agent in the conjugated or unconjugated compositionsaccording to this aspect of the invention is a nucleic acid molecule.The nucleic acid may be RNA or preferably DNA. In some embodiments, thenucleic acid molecule is an antisense molecule or encodes an antisensesequence whose presence in the cell inhibits production of anundesirable protein. In some embodiments, the nucleic acid moleculeencodes a ribozyme whose presence in the cell inhibits production of anundesirable protein. In some embodiments, the nucleic acid moleculeencodes a protein or peptide that is desirably produced in the cell. Insome embodiments, the nucleic acid molecule encodes a functional copy ofa gene that is defective in the targeted cell. The nucleic acid moleculeis preferably operably linked to regulatory elements needed to expressthe coding sequence in the cell.

Liposomes are small vesicles composed of lipids. Genetic constructswhich encode proteins that are desired to be expressed in CRCA-1translation product-bearing cells are introduced into the center ofthese vesicles. The outer shell of these vesicles comprise an a CRCA-1translation product ligand. Liposomes Volumes 1, 2 and 3 CRC Press Inc.Boca Raton FLA, which is incorporated herein by reference, disclosepreparation of liposome-encapsulated active agents which includeantibodies in the outer shell. In the present invention, a CRCA-1translation product ligand such as for example an anti-CRCA-1translation product antibodies is associated with the in the outershell. Unconjugated compositions which comprise a CRCA-1 translationproduct ligand in the matrix of a liposome with an active agent insideinclude such compositions in which the CRCA-1 translation product ligandis preferably an antibody.

In one embodiment for example, cystic fibrosis, a genetic disease inwhich there is a mutation of a specific gene encoding a chloridetransport protein which ultimately produces abnormalities of function inmany systems, most notably in the respiratory and intestinal tract, istreated by gene therapy techniques using CRCA-1 translation productligands to deliver the corrective gene to cells. Current therapy hasbeen directed at replacing the mutant gene in the respiratory systemwith the normal gene by targeting these genes directly to the cellslining the respiratory tract using viruses which bind only to thosecells. Similarly, the normal gene is packaged in liposomes targeted ontheir surface with CRCA-1 translation product ligands and delivered tothe intestinal tract. CRCA-1 translation product ligands specificallytarget and direct the liposomes containing the normal gene to correctthe lesion for cystic fibrosis to the specific cells lining theintestinal tract, from the duodenum to the rectum. Uptake of thatgenetic material by those cells should result in a cure of cysticfibrosis in the intestinal tract.

In another embodiment, the delivery of normal copies of the p53 tumorsuppressor gene to the intestinal tract is accomplished using CRCA-1translation product ligand to target the gene therapeutic. Mutations ofthe p53 tumor suppressor gene appears to play a prominent role in thedevelopment of colorectal cancer in the intestinal tract. One approachto combatting this disease is the delivery of normal copies of this geneto the intestinal tract to cells expressing mutant forms of this gene.Genetic constructs that comprise normal p53 tumor suppressor genes areincorporated into liposomes that comprise a CRCA-1 translation productligand. The composition is delivered to the intestinal tract. CRCA-1translation product binding ligands specifically target and direct theliposomes containing the normal gene to correct the lesion created bymutation of p53 suppressor gene in intestinal cells.

Preparation of genetic constructs is with the skill of those havingordinary skill in the art. The present invention allows such constructto be specifically targeted by using the CRCA-1 translation productligands of the present invention. The compositions of the inventioninclude a CRCA-1 translation product ligand such as an anti-CRCA-1translation product antibody associated with a delivery vehicle and agene construct which comprises a coding sequence for a protein whoseproduction is desired in the cells of the intestinal tract linked tonecessary regulatory sequences for expression in the cells. For uptakeby cells of the intestinal tract, the compositions are administeredorally or by enema whereby they enter the intestinal tract and contactcells which comprise one or more CRCA-1 translation products. Thedelivery vehicles associate with the CRCA-1 translation product byvirtue of the CRCA-1 translation product ligand and the vehicle isinternalized into the cell or the active agent/genetic construct isotherwise taken up by the cell. Once internalized, the construct canprovide a therapeutic effect on the individual. One having ordinaryskill in the art can readily formulate such compositions for oral orenema administration and determine the effective amount of suchcomposition to be administered to treat the disease or disorder.

Antisense

The present invention procvides compositions, kits and methods which areuseful to prevent and treat diseases effecting colon cells by providingthe means to specifically deliver antisense compounds to colon cells andthereby stop expression of genes in such colon cells in whichundesirable gene expression is taking place without negatively effectingcells in which no such expression occurs.

The conjugated compositions of the present invention are useful fortargeting cells that line the inner intestine wall including thosecancer cells derived from such cells, including metastasized cancercells as well as localized cancer and normal colon cells. The conjugatedcompositions will not bind to non-colorectal derived cells. Thus, theactive moieties of conjugated compositions administered to an individualare delivered to cells which are derived from the intestinal tract suchas local normal and cancerous colorectal cells and metastasizedcolorectal cells. Non-colorectal cells, lacking one or more CRCA-1translation products, do not take up the conjugated compositions. Thus,the present invention provides compositions and methods of deliveringantisense compositions to colon cells only.

The present invention provides a colorectal cancer specific approach inwhich only colorectal cells are exposed to the active portion of thecompound and only colorectal cancer cells are effected by the conjugatedcompound. The ST receptor binding moiety specifically binds tocolorectal cells, including normal colorectal cells, localizedcolorectal cancer cells and metastasized colorectal cancer cells. Uponbinding to these cells, the conjugated compound is internalized and thedelivery of the conjugated compound including the antisense portion ofthe molecule is effected. The presence of the conjugated compound innormal colorectal cells has no effect on such cells because thecolorectal cancer-associated gene for which the antisense molecule thatmakes up the active moiety of the conjugated compound is complementaryis not being expressed. However, in colorectal cancer cells, the cancergene for which the antisense molecule that makes up the active moiety ofthe conjugated compound is complementary is being expressed. Thepresence of the conjugated compound in colorectal cancer cells serves toinhibit or prevent transcription or translation of the cancer gene andthereby reduce or eliminate the transformed phenotype.

The invention can be used to combat localized or metastasized colorectalcancer as well as to prevent the emergence of the transformed phenotype.Thus the invention can be used therapeutically as well asprophylactically.

Therapeutic and prophylactic pharmaceutical compositions of the presentinvention include conjugated compounds specifically targeted to coloncells. These conjugated compounds include CRCA-1 translation productsbinding moieties which do not bind to cells of normal tissue in the bodyexcept cells of the intestinal tract since the cells of other tissues donot possess ST receptors. Thus, only normal colorectal cells, localizedcolorectal cancer cells and metastasized colorectal cancer cells take upthe conjugated compositions.

One having ordinary skill in the art can readily identify individualssuspected of suffering from colorectal cancer and metastasizedcolorectal cells. In those individuals diagnosed with colorectal cancer,it is standard therapy to suspect metastasis and aggressively attempt toeradicate metastasized cells. The present invention providespharmaceutical compositions and methods for specifically targeting andeliminating metastasized colorectal cancer cells. Further, the presentinvention provides pharmaceutical compositions that comprisetherapeutics and methods for specifically eliminating colorectal cancercells. The present invention provides pharmaceutical compositions andmethods for specifically in colorectal cells and preventingtransformation by such cells by prophylactically furnishing such cellswith antisense molecules that inhibit transcription or translation ofgenes involved in transformation.

The pharmaceutical compositions which comprise conjugated compositionsof the present invention may be used to diagnose or treat individualssuffering from localized and/or metastatic colorectal tumors, that isprimary or non-metastatic colorectal tumors as well as metastasizedcolorectal tumors.

The present invention relies upon the use of a CRCA-1 translationproduct binding moiety in a conjugated composition. The CRCA-1translation product binding moiety is essentially a portion of theconjugated composition which acts as a ligand to the CRCA-1 translationproduct and thus specifically binds to these receptors. The conjugatedcomposition also includes an active moiety which is associated with theCRCA-1 translation product binding moiety; the active moiety being anantisense composition useful to inhibit or prevent transcription ortranslation of expression of genes whose expression is associated withcancer.

According to the present invention, the active moiety is an antisensecomposition. In particular, the antisense molecule that makes up theactive moiety of a conjugated compound hybridizes to DNA or RNA in acolon cell and inhibits and/or prevents transcription or translation ofthe DNA or RNA from taking place. The antisense compositions may be anucleic acid molecule, a derivative or an analogs thereof. The chemicalnature of the antisense composition may be that of a nucleic acidmolecule or a modified nucleic acid molecule or a non-nucleic acidmolecule which possess functional groups that mimic a DNA or RNAmolecule that is complementary to the DNA or RNA molecule whoseexpression is to be inhibited or otherwise prevented. Antisensecompositions inhibit or prevent transcription or translation of geneswhose expression is linked to colorectal cancer, i.e. colorectal cancerassociated genes. Examples of such genes include, but are not limitedto: hereditary nonpolyposis coli (HNPCC) genes such as hMSH2, hMLH1,hPMS1, and hPMS2, Ras, adenomatous polyposis coli (APC), ERBB-1/HER-1,ERBB-2/HER-2, p53 Tumor Suppressor, MYB, FOS, ABL, MYC, Protein TyrosinePhosphatase G1, Cyclic AMP-Dependent Protein Kinase (PKA), CRIPTO,Transforming Growth Factor Alpha and 1p.

Colorectal cancer-associated genes provide the genetic basis forcolorectal cancer. Colorectal cancer is a process involving accumulationof genetic mutations in epithelial cells leading to the neoplasticphenotype associated with unregulated growth. Colorectal carcinogenesisis a multistage process involving the progression from adenomas toinvasive carcinomas. Indeed, the cumulative total of geneticabnormalities appear to be more important than their order ofappearance. Many of the genetic abnormalities result from allelic lossor deletion of fragments of chromosomes. Specific genetic abnormalitieswhich have been associated with the colorectal cancer phenotype will bediscussed below. These all are potential s for treatment employinggenetic approaches. See: Toribara, NW and Sleisenger, MH (1995)Screening for colorectal cancer. New Eng. J. Med. 332:861–867 which ishereby incorporated herein by reference including all references citedtherein which are also hereby incorporated herein by reference.

HNPCC refers to 4 genes that are suspected to be responsible forhereditary nonpolyposis coli (HNPCC) colorectal cancer. These four geneshave been identified and are discussed in Toribara, NW and Sleisenger,MH (1995) Screening for colorectal cancer. New Eng. J. Med. 332:861–867.The genes, called hMSH2, hMLH1, hPMS1, and hPMS2, are proofreading genesthat repair mismatches of bases in DNA. Loss of this function allowsreplication errors to occur in the DNA.

Point mutations insertions, and deletions in K-ras and H-ras have beenidentified in colorectal tumors. See: Toribara, N W and Sleisenger, M H(1995) Screening for colorectal cancer. New Eng. J. Med. 332:861–867;Kniazev, P G, et al. Complex characteristics of the alterations ofoncogenes HER-2/ERBB-2, HER-1/ERBB-1, HRAS-1, C-MYC and anti-oncogenesp53, RB1, as well as deletions of loci of chromosome 17 in coloncarcinoma. Molekuliarnaia Biologiia. 26(5):1134–47, 1992,September–October and Ramsay, R G, et al. Myb expression is higher inmalignant human colonic carcinoma and premalignant adenomatous polypsthan in normal mucosa. Cell Growth & Differentiation. 3(10):723–30, 1992October, which are each hereby incorporated herein by referenceincluding all references cited therein which are also herebyincorporated herein by reference.

Patients with familial adenomatous polyposis coli (APC) appear to have aseries of deletions including deletions of chromosome 5q, 18q, 17p. The17p deletion represents a deletion of the p53 suppressor gene.

ERBB-1/HER-1 and ERBB-2/HER-2 genes have been demonstrated to beamplified in about 4–8% of cases of colorectal cancer.

Point mutations in p53 genes have been reported to be mutated in about3% of colorectal cancer cases.

MYB proto-oncogene expression has been demonstrated to be higher incolorectal tumors. See: Ramsay, R G, Thompson, M A, Hayman, J A, Reid,G, Gonda, T J, Whitehead, R H. Myb expression is higher in malignanthuman colonic carcinoma and premalignant adenomatous polyps than innormal mucosa. Cell Growth & Differentiation. 3(10):723–30, 1992October; Melani, C. et al. Inhibition of proliferation by c-mybantisense oligodeoxynucleotides in colon adenocarcinoma cell lines thatexpress c-myb. Cancer Research 51(11):2897–901, 1991, Jun. 1; and RamsayR G, et al. Myb expression is higher in malignant human coloniccarcinoma and premalignant adenomatous polyps than in normal mucosa.Cell Growth & Differentiation. 3 (10):723–30, 1992 October; which areeach hereby incorporated herein by reference including all referencescited therein which are also hereby incorporated herein by reference.Indeed, tumors and cells with the highest levels of expression of MYBwere the most dysplastic and had the highest levels of proliferation.cMYB is a protooncogene which plays a role in the proliferationsignaling pathway. Rearrangements, insertions, and deletions of thisgene have been observed. See: Alexander, R J, et al. Oncogenealterations in rat colon tumors induced by N-methyl-N-nitrosourea.American Journal of the Medical Sciences. 303(1):16–24, 1992, Januarywhich is hereby incorporated herein by reference including allreferences cited therein which are also hereby incorporated herein byreference. Antisense MYB oligonucleotides retard the proliferation ofcolonic adenocarcinoma cells which had the highest level of expressionof this oncogene, in vitro.

Chemical carcinogenesis in a rat model demonstrated point mutations infos, an oncogene which mediates transcriptional regulation andproliferation. See: Alexander, R J, et al. Oncogene alterations in ratcolon tumors induced by N-methyl-N-nitrosourea. American Journal of theMedical Sciences. 303(1):16–24, 1992, January which is herebyincorporated herein by reference including all references cited thereinwhich are also hereby incorporated herein by reference.

Chemical carcinogenesis in a rat model demonstrated point mutations inthe oncogene abl. See: Alexander, R J, et al. Oncogene alterations inrat colon tumors induced by N-methyl-N-nitrosourea. American Journal ofthe Medical Sciences. 303(1):16–24, 1992, Jan.

MYC is an oncogene that plays a role in regulating transcription andproliferation. Increased expression of MYC has been found in colorectalcancer cells. Collins, J F, et al. c-myc antisense oligonucleotidesinhibit the colony-forming capacity of Colo 320 colonic carcinoma cells.Journal of Clinical Investigation. 89 (5):1523–7, 1992 May; andRodriguez-Alfageme, C, et al. Suppression of deregulated c-MYCexpression in human colon carcinoma cells by chromosome 5 transfer.Proceedings of the National Academy of Sciences of the United States ofAmerica. 89(4):1482–6, 1992 Feb. 15. which are both hereby incorporatedherein by reference including all references cited therein which arealso hereby incorporated herein by reference. A 15-base antisenseoligonucleotide to myc complementary to the translation initiationregion of exon II was incubated with colorectal cancer cells. Thisantisense molecule inhibited proliferation of colorectal cancer cells ina dos-dependent fashion. Interestingly, the uptake of thisoligonucleotide was low (0.7%). Also, transfer of a normal chromosome 5to colorectal cancer cells resulted in the regulation of myc expressionand loss of proliferation. These data suggest that a tumor suppressorgene important in the regulation of myc is contained on this chromosome.

A novel protein tyrosine phosphatase, G1, has been identified.Examination of the mRNA encoding this protein in colorectal tumor cellsrevealed that it undergoes point mutations and deletions in these cellsand may play a role in proliferation characteristic of these cells.Takekawa, M. et al. Chromosomal localization of the protein tyrosinephosphatase G1 gene and characterization of the aberrant transcripts inhuman colon cancer cells. FEBS Letters. 339(3):222–8, 1994 Feb. 21,which is hereby incorporated herein by reference including allreferences cited therein which are also hereby incorporated herein byreference.

Gastrin regulates colon cancer cell growth through a cyclicAMP-dependent mechanism mediated by PKA. Antisense oligodeoxynucleotidesto the regulatory subunit of a specific class of PKA inhibited thegrowth-promoting effects of cyclic AMP in colon carcinoma cells. See:Bold, R J, et al. Experimental gene therapy of human colon cancer.Surgery. 116(2):189–95; discussion 195–6, 1994 August and Yokozaki, H.,et al. An antisense oligodeoxynucleotide that depletes RI alpha subunitof cyclic AMP-dependent protein kinase induces growth inhibition inhuman cancer cells. Cancer Research. 53(4):868–72, 1993 Feb. 15, whichare both hereby incorporated herein by reference including allreferences cited therein which are also hereby incorporated herein byreference.

CRIPTO is an epidermal growth factor-related gene expressed in amajority of colorectal cancer tumors. Antisense phosphorothioateoligodeoxynucleotides to the 5′-end of CRIPTO mRNA significantly reducedCRIPTO expression and inhibited colorectal tumor cell growth in vitroand in vivo. Ciardiello, F. et al. Inhibition of CRIPTO expression andtumorigenicity in human colon cancer cells by antisense RNA andoligodeoxynucleotides. Oncogene. 9(1):291–8, 1994 January which are bothhereby incorporated herein by reference including all references citedtherein which are also hereby incorporated herein by reference.

Many carcinoma cells secrete transforming growth factor alpha. A 23nucleotide antisense oligonucleotide to TGF alpha mRNA inhibited bothDNA synthesis an proliferation of colorectal cancer cells. Sizeland, AM,Burgess, AW. Antisense transforming growth factor alpha oligonucleotidesinhibit autocrine stimulated proliferation of a colon carcinoma cellline. Molecular Biology of the Cell. 3(11):1235–43, 1992 November whichis hereby incorporated herein by reference including all referencescited therein which are also hereby incorporated herein by reference.

Human colorectal tumors have been identified with deletions ofchromosome 1p. It appears that a portion of this chromosome, 1p36–34,contains a tumor suppressor gene that regulates the expression of MYC.Tanaka, K, et al. Suppression of tumorigenicity in human colon carcinomacells by introduction of normal chromosome 1p36 region. Oncogene.8(8):2253–8, 1993 August, which is hereby incorporated herein byreference including all references cited therein which are also herebyincorporated herein by reference.

Antisense compositions including oligonucleotides, derivatives andanalogs thereof, conjugation protocols, and antisense strategies forinhibition of transcription and translation are generally described in:Antisense Research and Applications, Crooke, S. and B. Lebleu, eds. CRCPress, Inc. Boca Raton FLA 1993; Nucleic Acids in Chemistry and BiologyBlackburn, G. and M. J. Gait, eds. IRL Press at Oxford University Press,Inc. New York 1990; and Oligonucleotides and Analogues: A PracticalApproach Eckstein, F. ed., IRL Press at Oxford University Press, Inc.New York 1991 which are each hereby incorporated herein by referenceincluding all references cited therein which are hereby incorporatedherein by reference.

The antisense molecules of the present invention comprise a sequencecomplementary to a fragment of a colorectal cancer gene. See Ullrich etal., EMBO J., 1986, 5:2503, which is hereby incorporated herein byreference. Contemplated by this definition are fragments of oligoswithin the coding sequence of colorectal cancer genes.

Antisense compositions which can make up an active moiety in conjugatedcompounds of the invention include oligonucleotides formed ofhomopyrimidines can recognize local stretches of homopurines in the DNAdouble helix and bind to them in the major groove to form a triplehelix. See: Helen, C and Toulme, JJ. Specific regulation of geneexpression by antisense, sense, and antigene nucleic acids. Biochem.Biophys Acta, 1049:99–125, 1990 which is hereby incorporated herein byreference including all references cited therein which are herebyincorporated herein by reference. Formation of the triple helix wouldinterrupt the ability of the specific gene to undergo transcription byRNA polymerase. Triple helix formation using myc-specificoligonucleotides has been observed. See: Cooney, M, et al. Science241:456–459 which is hereby incorporated herein by reference includingall references cited therein which are hereby incorporated herein byreference.

Antisense oligonucleotides of DNA or RNA complementary to sequences atthe boundary between introns and exons can be employed to prevent thematuration of newly-generated nuclear RNA transcripts of specific genesinto mRNA for transcription.

Antisense RNA complementary to specific genes can hybridize with themRNA for tat gene and prevent its translation. Antisense RNA can beprovided to the cell as “ready-to-use” RNA synthesized in vitro or as anantisense gene stably transfected into cells which will yield antisenseRNA upon transcription. Hybridization with mRNA results in degradationof the hybridized molecule by RNAse H and/or inhibition of the formationof translation complexes. Both result in a failure to produce theproduct of the original gene.

Antisense sequences of DNA or RNA can be delivered to cells. Severalchemical modifications have been developed to prolong the stability andimprove the function of these molecules without interfering in theirability to recognize specific sequences. These include increasing theirresistance to degradation by DNases, including phosphotriesters,methylphosphonates, phosphorothioates, alpha-anomers, increasing theiraffinity for their s by covalent linkage to various intercalating agentssuch as psoralens, and increasing uptake by cells by conjugation tovarious groups including polylysine. These molecules recognize specificsequences encoded in mRNA and their hybridization prevents translationof and increases the degradation of these messages.

Conjugated compositions of the invention provide a specific andeffective means for terminating the expression of genes which causeneoplastic transformation. CRCA-1 translation products undergoligand-induced endocytosis and can deliver conjugated compounds to thecytoplasm of cells when the CRCA-1 translation product binding moietybinds to an ST receptor on a colon cell. The unique localization ofthese receptors and their ability to undergo endocytosis make themexcellent candidates for targeting therapeutics to these tumors.

CRCA-1 translation product binding moieties are conjugated directly toantisense compositions such as nucleic acids which are active ininducing a response in colorectal tumor cells. For example, antisenseoligonucleotides to MYC are conjugated directly to an anti-CRCA-1translation product antibody. This has been performed employing peptidesthat bind to the CD4 receptor. See: Cohen, J S, ed.Oligodeoxynucleotides: Antisense Inhibitors of Gene Expression. Topicsin Molecular and Structural Biology. CRC Press, Inc., Boca Raton, 1989.which is hereby incorporated herein by reference including allreferences cited therein which are hereby incorporated herein byreference. The precise backbone and its synthesis is not specified andcan be selected from well-established techniques. Synthesis wouldinvolve either chemical conjugation or direct synthesis of the chimericmolecule by solid phase synthesis employing FMOC chemistry. See:Haralambidis, J, et al. (1987) Tetrahedron Lett. 28:5199–5202, which ishereby incorporated herein by reference including all references citedtherein which are hereby incorporated herein by reference.Alternatively, the peptide-nucleic acid conjugate may be synthesizeddirectly by solid phase synthesis as a peptide—peptide nucleic acidchimera by solid phase synthesis. Nielsen, P E, et al. (1994)Sequence-specific transcription arrest by peptide nucleic acid bound tothe DNA template strand. Gene 149:139–145, which is hereby incorporatedherein by reference including all references cited therein which arehereby incorporated herein by reference.

In some embodiments, polylysine can be complexed to conjugatedcompositions of the invention in a non-covalent fashion to nucleic acidsand used to enhance delivery of these molecules to the cytoplasm ofcells. In addition, peptides and proteins can be conjugated topolylysine in a covalent fashion and this conjugate complexed withnucleic acids in a non-covalent fashion to further enhance thespecificity and efficiency of uptake of the nucleic acids into cells.Thus, CRCA-1 translation product ligand is conjugated chemically topolylysine by established techniques. The polylysine-CRCA-1 translationproduct ligand conjugate may be complexed with nucleic acids of choice.Thus, polylysine-orosomucoid conjugates were employed to specificallyplasmids containing genes to be expressed to hepatoma cells expressingthe orosomucoid receptor. This approach can be used to delivery wholegenes, or oligonucleotides. Thus, it has the potential to terminate theexpression of an undesired gene (eg. MYC, ras) or replace the functionof a lost or deleted gene (eg. hMSH2, hMLH1, hPMS1, and hPMS2).

According to a preferred embodiment, Myc serves as a gene whoseexpression is inhibited by an antisense molecule within a conjugatedcomposition. Many, if not most, colorectal tumor cells overexpress MYC,a gene involved in mediating proliferation. Decreasing the proliferationof colorectal tumor cells is attained by employing antisenseoligonucleotides complementary to MYC to hybridize with the mRNA forthis protein, resulting in the degradation of this message and adramatic reduction in the production of MYC. CRCA-1 translation productbinding moieties are used to deliver a 15-based antisenseoligonucleotide to myc complementary to the translation initiationregion of exon II. This construct was active in inhibiting theexpression of MYC when it was incubated with colorectal cancer cells.The 15-base antisense oligonucleotide to MYC is synthesized as reportedin Collins, JF, Herman, P, Schuch, C, Bagby G C, Jr. Journal of ClinicalInvestigation. 89(5):1523–7, 1992 May. In some embodiments, theconjugated composition is conjugated to polylysine as reportedpreviously. Wu, GY, and Wu, CH. (1988) Evidence for ed gene delivery toHep G2 hepatoma cells in vitro. Biochem. 27:887–892 which isincorporated herein by reference.

Conjugated compositions may be synthesized as a chimeric moleculedirectly by solid phase synthesis. pmolar to nanomolar concentrationsfor this conjugate suppress MYC synthesis in colorectal cancer cells invitro.

Antisense molecules are preferably hybridize to, i.e. are complementaryto, a nucleotide sequence that is 5–50 nucleotides in length, morepreferably 5–25 nucleotides and in some embodiments 10–15 nucleotides.

In addition, mismatches within the sequences identified above, whichachieve the methods of the invention, such that the mismatched sequencesare substantially complementary to the colorectal cancer gene sequencesare also considered within the scope of the disclosure. Mismatches whichpermit substantial complementarity to the colorectal cancer genesequences will be known to those of skill in the art once armed with thepresent disclosure. The oligos may also be unmodified or modified.

Therapeutic compositions and methods may be used to combat colorectalcancer in cases where the cancer is localized and/or metastasized.Individuals are administered a therapeutically effective amount ofconjugated compound. A therapeutically effective amount is an amountwhich is effective to cause a cytotoxic or cytostatic effect onmetastasized colorectal cancer cells without causing lethal side effectson the individual. An individual who has been administered atherapeutically effective amount of a conjugated composition has aincreased chance of eliminating colon cancer as compared to the risk hadthe individual not received the therapeutically effective amount.

To treat localized colorectal cancer, a therapeutically effective amountof a conjugated compound is administered such that it will come intocontact with the localized tumor within the colon. Thus, the conjugatedcompound is administered orally or rectally. In cases where conjugatedcompounds are orally administered, they are preferably enteric coated orotherwise formulated to avoid degradation by stomach acids. Entericformulations are described in U.S. Pat. No. 4,601,896, U.S. Pat. No.4,729,893, U.S. Pat. No. 4,849,227, U.S. Pat. No. 5,271,961, U.S. Pat.No. 5,350,741, and U.S. Pat. No. 5,399,347, which are each herebyincorporated herein by reference. Oral and rectal formulation are taughtin Remington's Pharmaceutical Sciences, 18th Edition, 1990, MackPublishing Co., Easton Pa. which is incorporated herein by reference.Alternative embodiments include sustained release formulations andimplant devices which provide continuous delivery of conjugatedcompositions to the colon.

The pharmaceutical compositions according to the present invention maybe administered as either a single dose or in multiple doses. Thepharmaceutical compositions of the present invention may be administeredeither as individual therapeutic agents or in combination with othertherapeutic agents. The treatments of the present invention may becombined with conventional therapies, which may be administeredsequentially or simultaneously.

The present invention is directed to a method of delivering antisensecompounds to colon cells and inhibiting expression of colorectal cancergenes in mammals. The methods comprise administering to a mammal aneffective amount of a conjugated composition which comprises a CRCA-1translation product binding moiety conjugated to an antisenseoligonucleotide having a sequence which is complementary to a region ofDNA or mRNA of a colorectal cancer gene.

The conjugated compounds may be administering to mammals in a mixturewith a pharmaceutically-acceptable carrier, selected with regard to theintended route of administration and the standard pharmaceuticalpractice. Dosages will be set with regard to weight, and clinicalcondition of the patient. The conjugated compositions of the presentinvention will be administered for a time sufficient for the mammals tobe free of undifferentiated cells and/or cells having an abnormalphenotype. In therapeutic methods treatment extends for a timesufficient to inhibit transformed cells from proliferating andconjugated compositions may be administered in conjunction with otherchemotherapeutic agents to manage and combat the patient's cancer.

The conjugated compounds of the invention may be employed in the methodof the invention singly or in combination with other compounds. Theamount to be administered will also depend on such factors as the age,weight, and clinical condition of the patient. See Gennaro, Alfonso,ed., Remington's Pharmaceutical Sciences, 18th Edition, 1990, MackPublishing Co., Easton Pa.

Prophylactic compositions and methods may be used to prevent the originof colorectal cancer. In particular, conjugated compounds may beadministered to an individual is suspected of being susceptible tocolorectal cancer. Using genotyping techniques, the specific nature ofan individuals susceptibility may be identified. That is, it may bepossible to determine what cancer gene will be associated withcolorectal cancer in an individual. For example, defects in the APC geneand kits for diagnosing the same are disclosed in U.S. Pat. No.5,352,775 which is hereby incorporated herein by reference. Similarly,defects in the MCC gene and kits for diagnosing the same are disclosedin U.S. Pat. No. 5,330,892 which is hereby incorporated herein byreference. In prophylactic methods, treatment extends continuously orsporadically from time to time for a time sufficient to inhibittransformation.

To prevent colorectal cancer, a prophylactically effective amount of aconjugated compound is administered such that it will come into contactwith and incorporated by normal colon cells. Thus, the conjugatedcompound is administered orally or rectally. In cases where conjugatedcompounds are orally administered, they are preferably enteric coated orotherwise formulated to avoid degradation by stomach acids as describedabove.

A prophylactically effective amount is an amount which is effective toprevent the initiation of transformation of colon cancer in cells. Anindividual who has been administered a prophylactically effective amountof a conjugated composition has a reduced risk of development of coloncancer as compared to the risk had the individual not received theprophylactically effective.

Therapeutic and Prophylactic Vaccines

The invention relates to prophylactic and therapeutic vaccines forprotecting individuals against metastatic colorectal cancer and fortreating individuals who are suffering from metastatic colorectalcancer.

According to the present invention, one or more of the CRCA-1translation products serves as a target against which a protective andtherapeutic immune response can be induced. Specifically, vaccines areprovided which induce an immune response against a CRCA-1 translationproduct. The vaccines of the invention include, but are not limited to,the following vaccine technologies:

1) DNA vaccines, i.e. vaccines in which DNA that encodes at least anepitope from a CRCA-1 translation product that is not present on STreceptor protein is administered to an individual's cells where theepitope is expressed and serves as a target for an immune response;

2) infectious vector mediated vaccines such as recombinant adenovirus,vaccinia, Salmonella, and BCG wherein the vector carries geneticinformation that encodes at least an epitope from a CRCA-1 translationproduct that is not present on ST receptor protein such that when theinfectious vector is administered to an individual, the epitope isexpressed and serves as a target for an immune response;

3) killed or inactivated vaccines which a) comprise either killed cellsor inactivated viral particles that display at least an epitope from aCRCA-1 translation product that is not present on ST receptor proteinand b) when administered to an individual serves as a target for animmune response;

3) haptenized killed or inactivated vaccines which a) comprise eitherkilled cells or inactivated viral particles that display at least anepitope from a CRCA-1 translation product that is not present on STreceptor protein, b) are haptenized to be more immunogenic and c) whenadministered to an individual serves as a target for an immune response;

4) subunit vaccines which are vaccines that include protein moleculesthat include at least an epitope from a CRCA-1 translation product thatis not present on ST receptor protein; and

5) haptenized subunit vaccines which are vaccines that a) includeprotein molecules that include at least an epitope from a CRCA-1translation product that is not present on ST receptor protein and b)are haptenized to be more immunogenic.

The present invention relates to administering to an individual aprotein or nucleic acid molecule that comprises or encodes,respectively, an immunogenic epitope against which an therapeutic andprophylactic immune response can be induced. Such epitopes are generallyat least 6–8 amino acids in length. The vaccines of the inventiontherefore comprise proteins which are at least, or nucleic acids whichencode at least, 6–8 amino acids in length from one or more CRCA-1translation products that is not present on ST receptor protein. Thevaccines of the invention may comprise proteins which are at least, ornucleic acids which encode at least 10 to about 1000 amino acids inlength. The vaccines of the invention may comprise proteins which are atleast, or nucleic acids which encode at least, about 25 to about 500amino acids in length. The vaccines of the invention may compriseproteins which are at least, or nucleic acids which encode at least,about 50 to about 400 amino acids in length. The vaccines of theinvention may comprise proteins which are at least, or nucleic acidswhich encode at least, about 100 to about 300 amino acids in length.

The present invention relates to compositions for and methods oftreating individuals who are known to have metastasized colorectalcancer. Metastasized colorectal cancer may be diagnosed by those havingordinary skill in the art using art accepted clinical and laboratorypathology protocols and/or those described in U.S. Ser. No. 08/141,892filed on Oct. 26, 1993, U.S. Ser. No. 08/305,056 filed on Sep. 13, 1994,and PCT Application Serial Number PCT/US94/12232 filed Oct. 26, 1994.The present invention provides an immunotherapeutic vaccine useful totreat individuals who have been diagnosed as suffering from metastasizedcolorectal cancer. The immunotherapeutic vaccines of the presentinvention may be administered in combination with other therapiesincluding, but not limited to those described in U.S. Ser. No.08/141,892 filed on Oct. 26, 1993, U.S. Ser. No. 08/305,056 filed onSep. 13, 1994, and PCT Application Serial Number PCT/US94/12232 filedOct. 26, 1994.

The present invention relates to compositions for and methods ofpreventing metastatic colorectal cancer in individual is suspected ofbeing susceptible to metastasized colorectal cancer. Such individualsinclude those whose family medical history indicates above averageincidence of colorectal cancer among family members and/or those whohave already developed colorectal cancer and have been effectivelytreated who therefore face a risk of relapse and recurrence. Suchindividuals include those which have been diagnosed as having colorectalcancer including localized only or localized and metastasized colorectalcancer which has been resected or otherwise treated. Such individualsalso include those with an elevated risk as ascertained by geneticevaluation. For example, individuals with APC mutations can beidentified following the U.S. Pat. No. 5,352,775 issued Oct. 4, 1992 toAlbertsen et al., which is incorporated herein by reference.Furthermore, such individuals include: those suffering from inflammatorybowel disease, particularly those with ulcerative colitis; those withcolonic polyps; those with familial adenomatous polyposis, a heritablemutation predisposing patients to develop large numbers of intestinalpolyps; those with Peutz-Jeghers syndrome; those with hereditarynonpolyposis coli, a heritable mutation which predisposes people todevelop colon carcinoma; those with Turcot syndrome-colon carcinoma inconjunction with independent tumors of the central nervous system; andindividuals engaging in rectal intercourse. The vaccines of the presentinvention may be to susceptible individuals prophylactically to preventand combat colorectal cancer metastasis.

The invention relates to compositions which are the active components ofsuch vaccines or required to make the active components, to methods ofmaking such compositions including the active components, and to methodsof making and using vaccines.

The nucleotide sequence of the CRCA-1 transcript is set forth as SEQ IDNO:1 and the amino acid sequences of the various translation productsare set forth in SEQ ID NOs:2–81. The present invention relates toisolated fragments of the CRCA-1 transcript that encode specific CRCA-1translation products.

The present invention relates to recombinant vectors, includingexpression vectors, that comprise the CRCA-1 transcript or a fragmentthereof. The present invention relates to recombinant vectors, inlcudingexpression vectors that comprise nucleotide sequences that encode aCRCA-1 translation product or a functional fragment thereof.

The present invention relates to host cells which comprise such vectorsand to methods of making CRCA-1 translation products using suchrecombinant cells.

The present invention relates to the isolated CRCA-1 transcript and tothe isolated CRCA-1 translation products and to isolated antibodiesspecific for such products and to hybridomas which produce suchantibodies.

The present invention relates to the isolated CRCA-1 translationproducts and functional fragments thereof. Accordingly, some aspects ofthe invention relate to isolated proteins that comprise at least oneepitope of a CRCA-1 translation product.

Some aspects of the invention relate to the above described isolatedproteins which are haptenized to render them more immunogenic. That is,some aspects of the invention relate to haptenized proteins thatcomprise at least one CRCA-1 translation product epitope.

Accordingly, some aspects of the invention relate to isolated nucleicacid molecules that encode proteins that comprise at least one CRCA-1translation product epitope.

Naked DNA vaccines are described in PCT/US90/01515, which isincorporated herein by reference. Others teach the use of liposomemediated DNA transfer, DNA delivery using microprojectiles (U.S. Pat.No. 4,945,050 issued Jul. 31, 1990 to Sanford et al., which isincorporated herein by reference), and DNA delivery usingelectroporation. In each case, the DNA may be plasmid DNA that isproduced in bacteria, isolated and administered to the animal to betreated. The plasmid DNA molecules are taken up by the cells of theanimal where the sequences that encode the protein of interest areexpressed. The protein thus produced provides a therapeutic orprophylactic effect on the animal.

The use of vectors including viral vectors and other means of deliveringnucleic acid molecules to cells of an individual in order to produce atherapeutic and/or prophylactic immunological effect on the individualare similarly well known. Recombinant vaccines that employ vacciniavectors are, for example, disclosed in U.S. Pat. No. 5,017,487 issuedMay 21, 1991 to Stunnenberg et al. which is incorporated herein byreference.

In some cases, tumor cells from the patient are killed or inactivatedand administered as a vaccine product. Berd et al. May 1986 CancerResearch 46:2572–2577 and Berd et al. May 1991 Cancer Research51:2731–2734, which are incorporated herein by reference, describes thepreparation and use of tumor cell based vaccine products. According tosome aspects of the present invention, the methods and techniquesdescribed in Berd et al. are adapted by using colorectal cancer cellsinstead of melanoma cells.

The manufacture and use of isolated translation products and fragmentsthereof useful for example as laboratory reagents or components ofsubunit vaccines are well known. One having ordinary skill in the artcan isolate the CRCA-1 transcript or the specific portion thereof thatencodes a CRCA-1 translation product or a fragment thereof. Onceisolated, the nucleic acid molecule can be inserted it into anexpression vector using standard techniques and readily availablestarting materials.

The recombinant expression vector that comprises a nucleotide sequencethat encodes the nucleic acid molecule that encodes a CRCA-1 translationproduct or a fragment thereof or a protein that comprises the CRCA-1translation product or a fragment thereof. The recombinant expressionvectors of the invention are useful for transforming hosts to preparerecombinant expression systems for preparing the isolated proteins ofthe invention.

The present invention relates to a host cell that comprises therecombinant expression vector that includes a nucleotide sequence thatencodes one or more CRCA-1 translation products or a fragment thereof ora protein that comprises one or more CRCA-1 translation products or afragment thereof. Host cells for use in well known recombinantexpression systems for production of proteins are well known and readilyavailable. Examples of host cells include bacteria cells such as E.coli, yeast cells such as S. cerevisiae, insect cells such as S.frugiperda, non-human mammalian tissue culture cells chinese hamsterovary (CHO) cells and human tissue culture cells such as HeLa cells.

The present invention relates to a transgenic non-human mammal thatcomprises the recombinant expression vector that comprises a nucleicacid sequence that encodes the proteins of the invention. Transgenicnon-human mammals useful to produce recombinant proteins are well knownas are the expression vectors necessary and the techniques forgenerating transgenic animals. Generally, the transgenic animalcomprises a recombinant expression vector in which the nucleotidesequence that encodes one or more CRCA-1 translation products or afragment thereof or a protein that comprises the one or more CRCA-1translation products or a fragment thereof operably linked to a mammarycell specific promoter whereby the coding sequence is only expressed inmammary cells and the recombinant protein so expressed is recovered fromthe animal's milk.

In some embodiments, for example, one having ordinary skill in the artcan, using well known techniques, insert such DNA molecules into acommercially available expression vector for use in well knownexpression systems such as those described herein.

The expression vector including the DNA that encodes a CRCA-1translation product or a functional fragment thereof or a protein thatcomprises a CRCA-1 translation product or a functional fragment thereofis used to transform the compatible host which is then cultured andmaintained under conditions wherein expression of the foreign DNA takesplace. The protein of the present invention thus produced is recoveredfrom the culture, either by lysing the cells or from the culture mediumas appropriate and known to those in the art. The methods of purifyingthe CRCA-1 translation products or a fragment thereof or a protein thatcomprises the same using antibodies which specifically bind to theprotein are well known. Antibodies which specifically bind to aparticular protein may be used to purify the protein from naturalsources using well known techniques and readily available startingmaterials. Such antibodies may also be used to purify the protein frommaterial present when producing the protein by recombinant DNAmethodology. The present invention relates to antibodies that bind to anepitope which is present on one or more CRCA-1 translation products or afragment thereof or a protein that comprises the same. Antibodies thatbind to an epitope which is present on the CRCA-1 translation productare useful to isolate and purify the protein from both natural sourcesor recombinant expression systems using well known techniques such asaffinity chromatography. Immunoaffinity techniques generally aredescribed in Waldman et al. 1991 Methods of Enzymol. 195:391–396, whichis incorporated herein by reference. Antibodies are useful to detect thepresence of such protein in a sample and to determine if cells areexpressing the protein. The production of antibodies and the proteinstructures of complete, intact antibodies, Fab fragments and F(ab)₂fragments and the organization of the genetic sequences that encode suchmolecules are well known and are described, for example, in Harlow, E.and D. Lane (1988) ANTIBODIES: A Laboratory Manual, Cold Spring HarborLaboratory, Cold Spring Harbor, N.Y. which is incorporated herein byreference.

In some embodiments of the invention, transgenic non-human animals aregenerated. The transgenic animals according to the invention containnculeotides that encode one or more CRCA-1 translation products or afragment thereof or a protein that comprises the same under theregulatory control of a mammary specific promoter. One having ordinaryskill in the art using standard techniques, such as those taught in U.S.Pat. No. 4,873,191 issued Oct. 10, 1989 to Wagner and U.S. Pat. No.4,736,866 issued Apr. 12, 1988 to Leder, both of which are incorporatedherein by reference, can produce transgenic animals which produce one ormore CRCA-1 translation products or a fragment thereof or a protein thatcomprises the same. Preferred animals are goats and rodents,particularly rats and mice.

In addition to producing these proteins by recombinant techniques,automated peptide synthesizers may also be employed to produce one ormore CRCA-1 translation products or a fragment thereof or a fragmentthereof or a protein that comprises the same. Such techniques are wellknown to those having ordinary skill in the art and are useful ifderivatives which have substitutions not provided for in DNA-encodedprotein production.

In some embodiments, the protein that makes up a subunit vaccine or thecells or particles of a killed or inactivated vaccine may be haptenizedto increase immunogenicity. In some cases, the haptenization is theconjugation of a larger molecular structure to one or more CRCA-1translation products or a fragment thereof or a protein that comprisesthe same. In some cases, tumor cells from the patient are killed andhaptenized as a means to make an effective vaccine product. In cases inwhich other cells, such as bacteria or eukaryotic cells which areprovided with the genetic information to make and display a CRCA-1translation product or a fragment thereof or a protein that comprisesthe same, are killed and used as the active vaccine component, suchcells are haptenized to increase immunogenicity. Haptenization is wellknown and can be readily performed.

Methods of haptenizing cells generally and tumor cells in particular aredescribed in Berd et al. May 1986 Cancer Research 46:2572–2577 and Berdet al. May 1991 Cancer Research 51:2731–2734, which are incorporatedherein by reference. Additional haptenization protocols are disclosed inMiller et al. 1976 J. Immunol. 117(5:1):1591–1526.

Haptenization compositions and methods which may be adapted to be usedto prepare haptenized CRCA-1 immunogens according to the presentinvention include those described in the following U.S. Patents whichare each incorporated herein by reference: U.S. Pat. No. 5,037,645issued Aug. 6, 1991 to Strahilevitz; U.S. Pat. No. 5,112,606 issued May12, 1992 to Shiosaka et al.; U.S. Pat. No. 4,526,716 issued Jul. 2, 1985to Stevens; U.S. Pat. No. 4,329,281 issued May 11, 1982 to Christensonet al.; and U.S. Pat. No. 4,022,878 issued May 10, 1977 to Gross.Peptide vaccines and methods of enhancing immunogenicity of peptideswhich may be adapted to modify CRCA-1 immunogens of the invention arealso described in Francis et al. 1989 Methods of Enzymol. 178:659–676,which is incorporated herein by reference. Sad et al. 1992 Immunolology76:599–603, which is incorporated herein by reference, teaches methodsof making immunotherapeutic vaccines by conjugating gonadotropinreleasing hormone to diphtheria toxoid. CRCA-1 immunogens may besimilarly conjugated to produce an immunotherapeutic vaccine of thepresent invention. MacLean et al. 1993 Cancer Immunol. Immunother.36:215–222, which is incorporated herein by reference, describesconjugation methodologies for producing immunotherapeutic vaccines whichmay be adaptable to produce an immunotherapeutic vaccine of the presentinvention. The hapten is keyhole limpet hemocyanin which may beconjugated to a CRCA-1 immunogen.

Vaccines according to some aspects of the invention comprise apharmaceutically acceptable carrier in combination with a CRCA-1immunogen. Pharmaceutical formulations are well known and pharmaceuticalcompositions comprising such proteins may be routinely formulated by onehaving ordinary skill in the art. Suitable pharmaceutical carriers aredescribed in Remington's Pharmaceutical Sciences, A. Osol, a standardreference text in this field, which is incorporated herein by reference.The present invention relates to an injectable pharmaceuticalcomposition that comprises a pharmaceutically acceptable carrier and aCRCA-1 immunogen. The CRCA-1 immunogen is preferably sterile andcombined with a sterile pharmaceutical carrier.

In some embodiments, for example, one or more CRCA-1 translationproducts or a fragment thereof or a fragment thereof or a protein thatcomprises the same can be formulated as a solution, suspension, emulsionor lyophilized powder in association with a pharmaceutically acceptablevehicle. Examples of such vehicles are water, saline, Ringer's solution,dextrose solution, and 5% human serum albumin. Liposomes and nonaqueousvehicles such as fixed oils may also be used. The vehicle or lyophilizedpowder may contain additives that maintain isotonicity (e.g., sodiumchloride, mannitol) and chemical stability (e.g., buffers andpreservatives). The formulation is sterilized by commonly usedtechniques.

An injectable composition may comprise the CRCA-1 immunogen in adiluting agent such as, for example, sterile water,electrolytes/dextrose, fatty oils of vegetable origin, fatty esters, orpolyols, such as propylene glycol and polyethylene glycol. Theinjectable must be sterile and free of pyrogens.

The vaccines of the present invention may be administered by any meansthat enables the immunogenic agent to be presented to the body's immunesystem for recognition and induction of an immunogenic response.Pharmaceutical compositions may be administered parenterally, i.e.,intravenous, subcutaneous, intramuscular.

Dosage varies depending upon known factors such as the pharmacodynamiccharacteristics of the particular agent, and its mode and route ofadministration; age, health, and weight of the recipient; nature andextent of symptoms, kind of concurrent treatment, frequency oftreatment, and the effect desired. An amount of immunogen is deliveredto induce a protective or therapeutically effective immune response.Those having ordinary skill in the art can readily determine the rangeand optimal dosage by routine methods.

The following examples are illustrative but are not meant to be limitingof the present invention.

EXAMPLES Example 1

As stated above, a CRCA-1 translation product binding moiety is a CRCA-1translation product ligand that may be an antibody, a protein, apolypeptide, a peptide or a non-peptide. Peptides and non-peptide CCK Areceptor specific ligands may be identified using well known technology.

Over the past 10 years, it has become recognized that the specifichigh-affinity interaction of a receptor and a ligand, for example aCRCA-1 translation product and an anti-CRCA-1 translation productantibody, has its basis in the 3-dimensional conformational space of theligand and the complementary 3-dimensional configuration of the regionof the molecule involved in ligand binding. In addition, it has becomerecognized that various arrays of naturally-occurring amino acids,non-natural amino acids, and organic molecules can be organized inconfigurations that are unrelated to the natural ligands in their linearstructure, but resemble the 3-dimensional structure of the naturalligands in conformational space and, thus, are recognized by receptorswith high affinity and specificity. Furthermore, techniques have beendescribed in the literature that permit one of ordinary skill in the artto generate large libraries of these arrays of natural amino acids,non-natural amino acids and organic compounds to prospectively identifyindividual compounds that interact with receptors with high affinity andspecificity which are unrelated to the native ligand of that receptor.Thus, it is a relatively straightforward task for one of ordinary skillin the art to identify arrays of naturally occurring amino acids,non-natural amino acids, or organic compounds which can bindspecifically and tightly to the CRCA-1 translation product, which bearno structural relationship to an anti-CRCA-1 translation productantibody.

To identify CRCA-1 translation product ligands that are peptides, thosehaving ordinary skill in the art can use any of the well knownmethodologies for screening random peptide libraries in order toidentify peptides which bind to the CRCA-1 translation product. In themost basic of methodologies, the peptides which bind to the target areisolated and sequenced. In some methodologies, each random peptide islinked to a nucleic acid molecule which includes the coding sequence forthat particular random peptide. The random peptides, each with anattached coding sequence, are contacted with a CRCA-1 translationproduct and the peptides which are unbound to the CRCA-1 translationproduct are removed. The nucleic acid molecule which includes the codingsequence of the peptide that binds to the CRCA-1 translation product canthen be used to determine the amino acid sequence of the peptide as wellas produce large quantities of the peptide. It is also possible toproduce peptide libraries on solid supports where the spatial locationon the support corresponds to a specific synthesis and thereforespecific peptide. Such methods often use photolithography-like steps tocreate diverse peptide libraries on solid supports in which the spatialaddress on the support allows for the determination of the sequence.

The production of organic compound libraries on solid supports may alsobe used to produce combinatorial libraries of non-peptide compounds suchas oligonucleotides and sugars, for example. As in the case of peptidelibraries on solid supports, the spatial location on the supportcorresponds to a specific synthesis and therefore specific compound.Such methods often use photolithography-like steps to create diversecompound libraries on solid supports in which the spatial address on thesupport allows for the determination of the synthesis scheme whichproduced the compound. Once the synthesis scheme is identified, thestructure of the compound can become known.

Gallop et al. 1994 J. Medicinal Chemistry 37:1233, which is incorporatedherein by reference, provides a review of several of the variousmethodologies of screening random peptide libraries and identifyingpeptides from such libraries which bind to target proteins. Followingthese teachings, CRCA-1 translation product specific ligands that arepeptides and that are useful as CRCA-1 translation product specificbinding moieties may be identified by those having ordinary skill in theart.

Peptides and proteins displayed on phage particles are described inGallop et al. Supra. Random arrays of nucleic acids can be inserted intogenes encoding surface proteins of bacteriophage which are employed toinfect bacteria, yielding phage expressing the peptides encoded by therandom array of nucleotides on their surface. These phage displaying thepeptide can be employed to determine whether those peptides can bind tospecific proteins, receptors, antibodies, etc. The identity of thepeptide can be determined by sequencing the recombinant DNA from thephage expressing the peptide. This approach has the potential to yieldvast arrays of peptides in a library (up to 10⁹ unique peptides). Thistechnique has been employed to identify novel binding peptides to thefibrinogen receptor on platelets, which bear no sequence homology to thenatural occurring ligands of this receptor (Smith et al., 1993 Gene128:37, which is incorporated herein by reference). Similarly, thistechnique has been applied to identify peptides which bind to the MHCclass II receptor (Hammer et al., 1993 Cell 74:197, which isincorporated herein by reference) and the chaperonin receptor(Blond-Elguindi et al., 1993 Cell 75:717, which is incorporated hereinby reference).

Peptides displayed on plasmids are described in Gallop et al. Supra. Inthis approach, the random oligonucleotides which encode the library ofpeptides can be expressed on a specific plasmid whose expression isunder the control of a specific promoter, such as the lac operon. Thepeptides are expressed as fusion proteins coupled to the Lac I protein,under the control of the lac operon. The fusion protein specificallybinds to the lac operator on the plasmid and so the random peptide isassociated with the specific DNA element that encodes it. In this way,the sequence of the peptide can be deduced, by PCR of the DNA associatedwith the fusion protein. These proteins can be screened in solutionphase to determine whether they bind to specific receptors. Employingthis approach, novel substrates have been identified for specificenzymes (Schatz 1993).

A variation of the above technique, also described in Gallop et al.Supra, can be employed in which random oligonucleotides encoding peptidelibraries on plasmids can be expressed in cell-free systems. In thisapproach, a molecular DNA library can be constructed containing therandom array of oligonucleotides, which are then expressed in abacterial in vitro transcription/translation system. The identity of theligand is determined by purifying the complex of nascent chainpeptide/polysome containing the mRNA of interest on affinity resinscomposed of the receptor and then sequencing following amplificationwith RT-PCR. Employing this technique permits generation of largelibraries (up to 10¹¹ recombinants). Peptides which recognize antibodiesspecifically directed to dynorphin have been identified employing thistechnique (Cull et al., 1992 Proc. Natl. Acad. Sci. USA 89:1865, whichis incorporated herein by reference).

Libraries of peptides can be generated for screening against a receptorby chemical synthesis. For example, simultaneous preparation of largenumbers of diverse peptides have been generated employing the approachof multiple peptide synthesis as described in Gallop et al. Supra. Inone application, random peptides are generated by standard solid-phaseMerrifield synthesis on polyacrylamide microtiter plates (multipinsynthesis) which are subsequently screened for their ability to competewith receptor binding in a standard competitive binding assay (Wang etal., 1993 Bioorg. Med. Chem. Lett. 3:447, which is incorporated hereinby reference). Indeed, this approach has been employed to identify novelbinding peptides to the substance P receptor (Wang et al. Supra).Similarly, peptide libraries can be constructed by multiple peptidesynthesis employing the “tea bag” method in which bags of solid supportresin are sequentially incubated with various amino acids to generatearrays of different peptides (Gallop et al. Supra). Employing thisapproach, peptides which bind to the integrin receptor (Ruggeri et al.,1986 Proc. Natl. Acad. Sci. USA 83:5708, which is incorporated herein byreference) and the neuropeptide Y receptor (Beck-Sickinger et al., 1990Int. J. Peptide Protein Res. 36:522, which is incorporated herein byreference) have been identified.

In general, the generation and utility of combinatorial libraries dependon (1) a method to generate diverse arrays of building blocks, (2) amethod for identifying members of the array that yield the desiredfunction, and (3) a method for deconvoluting the structure of thatmember. Several approaches to these constraints have been defined.

The following is a description of methods of library generation whichcan be used in procedures for identifying CRCA-1 translation productspecific ligands according to the invention.

Modifications of the above approaches can be employed to generatelibraries of vast molecular diversity by connecting together members ofa set of chemical building blocks, such as amino acids, in all possiblecombinations (Gallop et al. Supra) In one approach, mixtures ofactivated monomers are coupled to a growing chain of amino acids on asolid support at each cycle. This is a multivalent synthetic system.

Also, split synthesis involves incubating the growing chain inindividual reactions containing only a single building block (Gallop etal. Supra). Following attachment, resin from all the reactions are mixedand apportioned into individual reactions for the next step of coupling.These approaches yield a stochastic collection of nx different peptidesfor screening, where n is the number of building blocks and x is thenumber of cycles of reaction.

Alternatively, arrays of molecules can be generated in which one or morepositions contain known amino acids, while the remainder are random(Gallop et al. Supra). These yield a limited library which is screenedfor members with the desired activity. These members are identified,their structure determined, and the structure regenerated with anotherposition containing defined amino acids and screened. This iterativeapproach ultimately yields peptides which are optimal for recognizingthe conformational binding pocket of a receptor.

In addition, arrays are not limited to amino acids forming peptides, butcan be extended to linear and nonlinear arrays of organic molecules(Gordon et al., 1994 J. Medicinal Chemistry 37:1385, which isincorporated herein by reference) Indeed, employing this approach ofgenerating libraries of randomly arrayed inorganic building blocks,ligands which bound to 7-transmembrane receptors were identified(Zuckermann et al., 1994 J. Med. Chem. 37:2678, which is incorporatedherein by reference).

Libraries are currently being constructed which can be modified aftersynthesis to alter the chemical side groups and bonds, to give“designer” arrays to test for their interaction with receptors (Ostereshet al., 1994 Proc. Natl. Acad. Sci. USA 91:11138, which is incorporatedherein by reference). This technique, generating “libraries fromlibraries”, was applied to the permethylation of a peptide library whichyielded compounds with selective antimicrobial activity against grampositive bacteria.

Libraries are also being constructed to express arrays ofpharmacological motifs, rather than specific structural arrays of aminoacids (Sepetov et al., 1995 Proc. Natl. Acad. Sci. USA 92:5426, which isincorporated herein by reference). This technique seeks to identifystructural motifs that have specific affinities for receptors, which canbe modified in further refinements employing libraries to definestructure-activity relationships. Employing this approach of searchingmotif libraries, generating “libraries of libraries”, reduces the numberof component members required for screening in the early phase oflibrary examination.

The following is a description of methods of identifying CRCA-1translation product specific ligands according to the invention fromlibraries of randomly generated molecules.

Components in the library which interact with receptors may beidentified by their binding to receptors immobilized on solid support(Gordon et al. Supra).

They may also be identified by their ability to compete with nativeligand for binding to cognate receptors in solution phase (Gordon et al.Supra).

Components may be identified by their binding to soluble receptors whenthose components are immobilized on solid supports (Gordon et al.Supra).

Once a member of a library which binds receptors has been identified,the structure of that member must be deconvoluted (deduced) in order toidentify the structure and generate large quantities to work with, ordevelop further analogs to study structure-activity relationships. Thefollowing is a description of methods of deconvolution for deducing thestructure of molecules identified as potential CRCA-1 translationproduct specific ligands according to the invention.

Peptide libraries may be expressed on the surface of bacteriophageparticles (Gallop et al. Supra). Once the peptide interacting with thereceptor has been identified, its structure can be deduced by isolatingthe DNA from the phage and determining its sequence by PCR.

Libraries expressed on plasmids, under the control of the Lac operon canbe deconvoluted since these peptides are fused with the lac I proteinwhich specifically interacts with the lac operon on the plasmid encodingthe peptide (Gallop et al. Supra) The structure can be deduced byisolating that plasmid attached to the lac I protein and deducing thenucleotide and peptide sequence by PCR.

Libraries expressed on plasmids can also be expressed in cell-freesystems employing transcription/translation systems (Gallop et al.Supra). In this paradigm, the protein interacting with receptors isisolated with its attached ribosome and mRNA. The sequence of thepeptide is deduced by RT-PCR of the associated mRNA.

Library construction can be coupled with photolithography, so that thestructure of any member of the library can be deduced by determining itsposition within the substrate array (Gallop et al. Supra). Thistechnique is termed positional addressability, since the structuralinformation can be deduced by the precise position of the member.

Members of a library can also be identified by tagging the library withidentifiable arrays of other molecules (Ohlmeyer et al., 1993 Proc.Natl. Acad. Sci. USA 90:10922, which is incorporated herein byreference, and Gallop et al. Supra). This technique is a modification ofassociating the peptide with the plasmid of phage encoding the sequence,described above. Some methods employ arrays of nucleotides to encode thesequential synthetic history of the peptide. Thus, nucleotides areattached to the growing peptide sequentially, and can be decoded by PCRto yield the structure of the associated peptide. Alternatively, arraysof small organic molecules can be employed as sequencable tags whichencode the sequential synthetic history of the peptide. Thus,nucleotides are attached to the growing peptide sequentially, and can bedecoded by PCR to yield the structure of the associated peptide.Alternatively, arrays of small organic molecules can be employed assequencable tags which encode the sequential synthetic history of thelibrary member.

Finally, the structure of a member of the library can be directlydetermined by amino acid sequence analysis.

The following patents, which are each incorporated herein by reference,describe methods of making random peptide or non-peptide libraries andscreening such libraries to identify compounds that bind to targetproteins. As used in the present invention, CRCA-1 translation productcan be the targets used to identify the peptide and non-peptide ligandsgenerated and screened as disclosed in the patents.

U.S. Pat. No. 5,270,170 issued to Schatz et al. on Dec. 14, 1993, andU.S. Pat. No. 5,338,665 issued to Schatz et al. on Aug. 16, 1994, whichare both incorporated herein by reference, refer to peptide librariesand screening methods which can be used to identify CRCA-1 translationproduct ligands.

U.S. Pat. No. 5,395,750 issued to Dillon et al. on Mar. 7, 1995, whichis incorporated herein by reference, refers to methods of producingproteins which bind to predetermined antigens. Such methods can be usedto produce CRCA-1 translation product ligands.

U.S. Pat. No. 5,223,409 issued to Ladner et al. on Jun. 29, 1993, whichis incorporated herein by reference, refers to the directed evolution tonovel binding proteins. Such proteins may be produced and screened asdisclosed therein to identify CRCA-1 translation product ligands.

U.S. Pat. No. 5,366,862 issued to Venton et al. on Nov. 22, 1994, whichis incorporated herein by reference, refers to methods for generatingand screening useful peptides. The methods herein described can be usedto identify CRCA-1 translation product ligands.

U.S. Pat. No. 5,340,474 issued to Kauvar on Aug. 23, 1994 as well asU.S. Pat. No. 5,133,866, U.S. Pat. No. 4,963,263 and U.S. Pat. No.5,217,869, which are each incorporated herein by reference, can be usedto identify CRCA-1 translation product ligands.

U.S. Pat. No. 5,405,783 issued to Pirrung et al. on Apr. 11, 1995, whichis incorporated herein by reference, refers to large scalephotolithographic solid phase synthesis of an array of polymers. Theteachings therein can be used to identify CRCA-1 translation productligands.

U.S. Pat. No. 5,143,854 issued to Pirrung et al. on Sep. 1, 1992, whichis incorporated herein by reference, refers to a large scalephotolithographic solid phase synthesis of polypeptides and receptorbinding screening thereof.

U.S. Pat. No. 5,384,261 issued to Winkler et al. on Jan. 24, 1995, whichis incorporated herein by reference, refers to very large scaleimmobilized polymer synthesis using mechanically directed flow patterns.Such methods are useful to identify CRCA-1 translation product ligands.

U.S. Pat. No. 5,221,736 issued to Coolidge et al. on Jun. 22, 1993,which is incorporated herein by reference, refers to sequential peptideand oligonucleotide synthesis using immunoaffinity techniques. Suchtechniques may be used to identify CRCA-1 translation product ligands.

U.S. Pat. No. 5,412,087 issued to McGall et al. on May 2, 1995, which isincorporated herein by reference, refers to spatially addressableimmobilization of oligonucleotides and other biological polymers onsurfaces. Such methods may be used to identify CRCA-1 translationproduct ligands.

U.S. Pat. No. 5,324,483 issued to Cody et al. on Jun. 28, 1994, which isincorporated herein by reference, refers to apparatus for multiplesimultaneous synthesis. The apparatus and method disclosed therein maybe used to produce multiple compounds which can be screened to identifyCRCA-1 translation product ligands.

U.S. Pat. No. 5,252,743 issued to Barrett et al. on Oct. 12, 1993, whichis incorporated herein by reference, refers to spatially addressableimmobilization of anti-ligands on surfaces. The methods and compositionsdescribed therein may be used to identify CRCA-1 translation productligands.

U.S. Pat. No. 5,424,186 issued to Foder et al. on Jun. 13, 1995, whichis incorporated herein by reference, refers to a very large scaleimmobilized polymer synthesis. The method of synthesizingoligonucleotides described therein may be used to identify CRCA-1translation product ligands.

U.S. Pat. No. 5,420,328 issued to Campbell on May 30, 1995, which isincorporated herein by reference, refers to methods of synthesis ofphosphonate esters. The phosphonate esters so produced may be screenedto identify compounds which are CRCA-1 translation product ligands.

U.S. Pat. No. 5,288,514 issued to Ellman on Feb. 22, 1994, which isincorporated herein by reference, refers to solid phase andcombinatorial synthesis of benzodiazepine compounds on a solid support.Such methods and compounds may be used to identify CRCA-1 translationproduct ligands.

As noted above, CRCA-1 translation product ligands may also beantibodies and fragments thereof. Indeed, antibodies raised to uniquedeterminants of these receptors will recognize that protein, and onlythat protein and, consequently, can serve as a specific targetingmolecule which can be used to direct novel diagnostics and therapeuticsto this unique marker. In addition, these antibodies can be used toidentify the presence of CRCA-1 translation product or fragments thereof in biological samples, to diagnose the presence of colorectal cancercells in vitro.

1. An isolated nucleic acid molecule consisting of a fragment of thenucleic acid sequence of SEQ ID NO:1 consisting of 30–200 nucleotidesincluding nucleotides 110–113 of SEQ ID NO:1.
 2. The nucleic acidmolecule of claim 1 consisting of 40–100 nucleotides.
 3. An isolatednucleic acid molecule consisting of the nucleic acid sequence of SEQ IDNO:1 or SEQ ID NO:2.
 4. An isolated recombinant vector comprising thenucleic acid molecule of claim
 3. 5. An isolated host cell comprisingthe recombinant vector of claim
 4. 6. The isolated nucleic acid of claim3 consisting of the nucleic acid sequence of SEQ ID NO:1.
 7. An isolatedoligonucleotide molecule that is the full complement of a fragment ofSEQ ID NO:1, said fragment consisting of 30–200 nucleotides of SEQ IDNO:1 including nucleotides 110–113 of SEQ ID NO:1.
 8. The isolatedoligonucleotide molecule of claim 7 consisting of 40–100 nucleotides. 9.An isolated oligonucleotide molecule that is the full complement of afragment of SEQ ID NO:1, said fragment comprising 18 nucleotides of SEQID NO:1 including nucleotides 110–113 of SEQ ID NO:1.
 10. Theoligonucleotide molecule of claim 9 consisting of 50 nucleotides.
 11. Anisolated oligonucleotide molecule comprising a nucleotide sequence thatis the full complement of a fragment of SEQ ID NO:1, said fragmentcomprising 18 nucleotides of SEQ ID NO:1 including nucleotides 110–113of SEQ ID NO:1; wherein said oligonucleotide molecule hybridizes to anucleic acid molecule consisting of SEQ ID NO:1 without hybridizing to anucleic acid molecule consisting of SEQ ID NO:83.
 12. The isolatedoligonucleotide molecule of claim 11 comprising 50 nucleotides.
 13. Theisolated oligonucleotide molecule of claim 11 comprising 40 nucleotides.14. The isolated oligonucleotide molecule of claim 11 comprising 25nucleotides.
 15. The isolated oligonucleotide molecule of claim 11comprising 150 nucleotides.
 16. The isolated oligonucleotide molecule ofclaim 11 comprising 28 nucleotides.
 17. An isolated nucleic acidmolecule that consists of SEQ ID NO:2.
 18. An isolated recombinantvector comprising the nucleic acid molecule of claim
 17. 19. An isolatedhost cell comprising the recombinant vector of claim 18.